@HD VN:1.5 SO:coordinate @RG ID:19727_1#11 PL:ILLUMINA CN:SC DT:2016-05-15T00:00:00+0100 LB:16416685 SM:EGAN00001402043 DS:EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PG:BamIndexDecoder PU:160515_HS36_19727_A_C7FVUANXX_1#11 @RG ID:19727_2#11 PL:ILLUMINA CN:SC DT:2016-05-15T00:00:00+0100 LB:16416685 SM:EGAN00001402043 DS:EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PG:BamIndexDecoder PU:160515_HS36_19727_A_C7FVUANXX_2#11 @RG ID:19727_3#11 PL:ILLUMINA CN:SC DT:2016-05-15T00:00:00+0100 LB:16416685 SM:EGAN00001402043 DS:EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PG:BamIndexDecoder PU:160515_HS36_19727_A_C7FVUANXX_3#11 @RG ID:19727_4#11 PL:ILLUMINA CN:SC DT:2016-05-15T00:00:00+0100 LB:16416685 SM:EGAN00001402043 DS:EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PG:BamIndexDecoder PU:160515_HS36_19727_A_C7FVUANXX_4#11 @PG ID:SCS_0 PN:HiSeq Control Software DS:Controlling software on instrument VN:2.2.68 @PG ID:basecalling_0 PN:RTA PP:SCS_0 DS:Basecalling Package VN:1.18.66.3 @PG ID:Illumina2bam_0 PN:Illumina2bam CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities BASECALLS_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout READ_GROUP_ID=19727_1 SAMPLE_ALIAS=EGAN00001402033,EGAN00001402034,EGAN00001402035,EGAN00001402036,EGAN00001402037,EGAN00001402038,EGAN00001402039,EGAN00001402040,EGAN00001402041,EGAN00001402042,EGAN00001402043,EGAN00001402044,EGAN00001402045,EGAN00001402046,EGAN00001402047,EGAN00001402048,EGAN00001402049,EGAN00001402050,EGAN00001402051,EGAN00001402052,EGAN00001402053,EGAN00001402054,EGAN00001402055,EGAN00001402056 STUDY_NAME=EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PLATFORM_UNIT=160515_HS36_19727_A_C7FVUANXX_1 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT ADD_CLUSTER_INDEX_TAG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:basecalling_0 DS:Convert Illumina BCL to BAM or SAM file VN:V1.19 @PG ID:bamadapterfind_0 PN:bamadapterfind CL:bamadapterfind level=0 PP:Illumina2bam_0 VN:2.0.43 @PG ID:BamIndexDecoder_0 PN:BamIndexDecoder CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/metadata_cache_19727/lane_1.taglist METRICS_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/19727_1.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=false BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false CHANGE_READ_NAME=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bamadapterfind_0 DS:A command-line tool to decode multiplexed bam file VN:V1.19 @PG ID:spf_0 PN:spatial_filter CL:/software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -c -F pb_align_19727_1.bam.filter -t /nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/qc/tileviz/19727_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_19727_1.bam ; /software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -a -f -u -F pb_align_19727_1.bam.filter - PP:BamIndexDecoder_0 DS:A program to apply a spatial filter VN:v10.26-dirty @PG ID:bwa_0 PN:bwa PP:spf_0 VN:0.5.10-tpx @PG ID:BamMerger_0 PN:BamMerger CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_19727_1.bam INPUT=/dev/stdin OUTPUT=19727_1.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bwa_0 DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.19 @PG ID:SplitBamByReadGroup_0 PN:SplitBamByReadGroup CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/19727_1.bam OUTPUT_PREFIX=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/lane1/ VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:BamMerger_0 DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.19 @PG ID:bamcollate2_0 PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamcollate2 collate=1 level=0 PP:SplitBamByReadGroup_0 VN:2.0.43 @PG ID:bamreset_0 PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamreset resetaux=0 level=0 verbose=0 PP:bamcollate2_0 VN:2.0.43 @PG ID:bamadapterclip_0 PN:bamadapterclip CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamadapterclip verbose=0 level=0 PP:bamreset_0 VN:2.0.43 @PG ID:bwa'_0 PN:bwa CL:/software/solexa/pkg/bwa/0.7.13/bwa mem -t 24 -p -T 0 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/JYv6_Ah81N/alntgt_bamtofastq_out PP:bamadapterclip_0 VN:0.7.13-r1126 @PG ID:scramble_0 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam PP:bwa'_0 VN:1.14.8 @PG ID:samtools_0 PN:samtools CL:/software/solexa/pkg/samtools/1.3.1-npg-Apr2016/bin/samtools reheader /tmp/sAoXNqgbW_/postalntgt_alterSQ_headerSQfix_out /tmp/PHqp9548cD/postalntgt_mbuffer_headerSQfix_out PP:scramble_0 VN:1.3.1-npg-Apr2016 @PG ID:bam12split_0 PN:bam12split CL:/software/solexa/pkg/biobambam/2.0.43/bin/bam12split verbose=0 level=0 PP:samtools_0 VN:2.0.43 @PG ID:bamsormadup_0 PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsormadup threads=24 SO=queryname level=0 PP:bam12split_0 VN:2.0.43 @PG ID:AlignmentFilter_0 PN:AlignmentFilter CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_19727_1#11.bam, /tmp/82mES5Ghtc/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/cu7PW7CO7N/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=19727_1#11.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:bamsormadup_0 DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file VN:V1.19 @PG ID:bamsort_0 PN:bamsort CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane1/bsfopt_19727_1#11.tmp PP:AlignmentFilter_0 VN:2.0.43 @PG ID:bamstreamingmarkduplicates_0 PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane1/bmdfopt_19727_1#11.tmp M=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane1/19727_1#11.markdups_metrics.txt PP:bamsort_0 VN:2.0.43 @PG ID:scramble.1_0 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -t 11 -7 -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa PP:bamstreamingmarkduplicates_0 VN:1.14.8 @PG ID:SCS_1 PN:HiSeq Control Software PP:scramble.1_0 DS:Controlling software on instrument VN:2.2.68 @PG ID:basecalling_1 PN:RTA PP:SCS_1 DS:Basecalling Package VN:1.18.66.3 @PG ID:Illumina2bam_1 PN:Illumina2bam CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities BASECALLS_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BaseCalls LANE=2 OUTPUT=/dev/stdout READ_GROUP_ID=19727_2 SAMPLE_ALIAS=EGAN00001402033,EGAN00001402034,EGAN00001402035,EGAN00001402036,EGAN00001402037,EGAN00001402038,EGAN00001402039,EGAN00001402040,EGAN00001402041,EGAN00001402042,EGAN00001402043,EGAN00001402044,EGAN00001402045,EGAN00001402046,EGAN00001402047,EGAN00001402048,EGAN00001402049,EGAN00001402050,EGAN00001402051,EGAN00001402052,EGAN00001402053,EGAN00001402054,EGAN00001402055,EGAN00001402056 STUDY_NAME=EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PLATFORM_UNIT=160515_HS36_19727_A_C7FVUANXX_2 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT ADD_CLUSTER_INDEX_TAG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:basecalling_1 DS:Convert Illumina BCL to BAM or SAM file VN:V1.19 @PG ID:bamadapterfind_1 PN:bamadapterfind CL:bamadapterfind level=0 PP:Illumina2bam_1 VN:2.0.43 @PG ID:BamIndexDecoder_1 PN:BamIndexDecoder CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/metadata_cache_19727/lane_2.taglist METRICS_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/19727_2.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=false BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false CHANGE_READ_NAME=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bamadapterfind_1 DS:A command-line tool to decode multiplexed bam file VN:V1.19 @PG ID:spf_1 PN:spatial_filter CL:/software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -c -F pb_align_19727_2.bam.filter -t /nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/qc/tileviz/19727_2 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_19727_2.bam ; /software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -a -f -u -F pb_align_19727_2.bam.filter - PP:BamIndexDecoder_1 DS:A program to apply a spatial filter VN:v10.26-dirty @PG ID:bwa_1 PN:bwa PP:spf_1 VN:0.5.10-tpx @PG ID:BamMerger_1 PN:BamMerger CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_19727_2.bam INPUT=/dev/stdin OUTPUT=19727_2.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bwa_1 DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.19 @PG ID:SplitBamByReadGroup_1 PN:SplitBamByReadGroup CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/19727_2.bam OUTPUT_PREFIX=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/lane2/ VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:BamMerger_1 DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.19 @PG ID:bamcollate2_1 PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamcollate2 collate=1 level=0 PP:SplitBamByReadGroup_1 VN:2.0.43 @PG ID:bamreset_1 PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamreset resetaux=0 level=0 verbose=0 PP:bamcollate2_1 VN:2.0.43 @PG ID:bamadapterclip_1 PN:bamadapterclip CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamadapterclip verbose=0 level=0 PP:bamreset_1 VN:2.0.43 @PG ID:bwa'_1 PN:bwa CL:/software/solexa/pkg/bwa/0.7.13/bwa mem -t 16 -p -T 0 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/0_vXIcnxMi/alntgt_bamtofastq_out PP:bamadapterclip_1 VN:0.7.13-r1126 @PG ID:scramble_1 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam PP:bwa'_1 VN:1.14.8 @PG ID:samtools_1 PN:samtools CL:/software/solexa/pkg/samtools/1.3.1-npg-Apr2016/bin/samtools reheader /tmp/5E2VWVdLkd/postalntgt_alterSQ_headerSQfix_out /tmp/p3lNM4QvZ9/postalntgt_mbuffer_headerSQfix_out PP:scramble_1 VN:1.3.1-npg-Apr2016 @PG ID:bam12split_1 PN:bam12split CL:/software/solexa/pkg/biobambam/2.0.43/bin/bam12split verbose=0 level=0 PP:samtools_1 VN:2.0.43 @PG ID:bamsormadup_1 PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsormadup threads=16 SO=queryname level=0 PP:bam12split_1 VN:2.0.43 @PG ID:AlignmentFilter_1 PN:AlignmentFilter CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_19727_2#11.bam, /tmp/Gx2HsXZfse/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/9pRjhu1EEy/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=19727_2#11.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:bamsormadup_1 DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file VN:V1.19 @PG ID:bamsort_1 PN:bamsort CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane2/bsfopt_19727_2#11.tmp PP:AlignmentFilter_1 VN:2.0.43 @PG ID:bamstreamingmarkduplicates_1 PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane2/bmdfopt_19727_2#11.tmp M=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane2/19727_2#11.markdups_metrics.txt PP:bamsort_1 VN:2.0.43 @PG ID:scramble.1_1 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -t 7 -7 -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa PP:bamstreamingmarkduplicates_1 VN:1.14.8 @PG ID:SCS_2 PN:HiSeq Control Software PP:scramble.1_1 DS:Controlling software on instrument VN:2.2.68 @PG ID:basecalling_2 PN:RTA PP:SCS_2 DS:Basecalling Package VN:1.18.66.3 @PG ID:Illumina2bam_2 PN:Illumina2bam CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities BASECALLS_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BaseCalls LANE=3 OUTPUT=/dev/stdout READ_GROUP_ID=19727_3 SAMPLE_ALIAS=EGAN00001402033,EGAN00001402034,EGAN00001402035,EGAN00001402036,EGAN00001402037,EGAN00001402038,EGAN00001402039,EGAN00001402040,EGAN00001402041,EGAN00001402042,EGAN00001402043,EGAN00001402044,EGAN00001402045,EGAN00001402046,EGAN00001402047,EGAN00001402048,EGAN00001402049,EGAN00001402050,EGAN00001402051,EGAN00001402052,EGAN00001402053,EGAN00001402054,EGAN00001402055,EGAN00001402056 STUDY_NAME=EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PLATFORM_UNIT=160515_HS36_19727_A_C7FVUANXX_3 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT ADD_CLUSTER_INDEX_TAG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:basecalling_2 DS:Convert Illumina BCL to BAM or SAM file VN:V1.19 @PG ID:bamadapterfind_2 PN:bamadapterfind CL:bamadapterfind level=0 PP:Illumina2bam_2 VN:2.0.43 @PG ID:BamIndexDecoder_2 PN:BamIndexDecoder CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/metadata_cache_19727/lane_3.taglist METRICS_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/19727_3.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=false BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false CHANGE_READ_NAME=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bamadapterfind_2 DS:A command-line tool to decode multiplexed bam file VN:V1.19 @PG ID:spf_2 PN:spatial_filter CL:/software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -c -F pb_align_19727_3.bam.filter -t /nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/qc/tileviz/19727_3 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_19727_3.bam ; /software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -a -f -u -F pb_align_19727_3.bam.filter - PP:BamIndexDecoder_2 DS:A program to apply a spatial filter VN:v10.26-dirty @PG ID:bwa_2 PN:bwa PP:spf_2 VN:0.5.10-tpx @PG ID:BamMerger_2 PN:BamMerger CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_19727_3.bam INPUT=/dev/stdin OUTPUT=19727_3.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bwa_2 DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.19 @PG ID:SplitBamByReadGroup_2 PN:SplitBamByReadGroup CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/19727_3.bam OUTPUT_PREFIX=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/lane3/ VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:BamMerger_2 DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.19 @PG ID:bamcollate2_2 PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamcollate2 collate=1 level=0 PP:SplitBamByReadGroup_2 VN:2.0.43 @PG ID:bamreset_2 PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamreset resetaux=0 level=0 verbose=0 PP:bamcollate2_2 VN:2.0.43 @PG ID:bamadapterclip_2 PN:bamadapterclip CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamadapterclip verbose=0 level=0 PP:bamreset_2 VN:2.0.43 @PG ID:bwa'_2 PN:bwa CL:/software/solexa/pkg/bwa/0.7.13/bwa mem -t 16 -p -T 0 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/TvcxvVVtkY/alntgt_bamtofastq_out PP:bamadapterclip_2 VN:0.7.13-r1126 @PG ID:scramble_2 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam PP:bwa'_2 VN:1.14.8 @PG ID:samtools_2 PN:samtools CL:/software/solexa/pkg/samtools/1.3.1-npg-Apr2016/bin/samtools reheader /tmp/3NuOWx9Kiu/postalntgt_alterSQ_headerSQfix_out /tmp/u8t30buuHa/postalntgt_mbuffer_headerSQfix_out PP:scramble_2 VN:1.3.1-npg-Apr2016 @PG ID:bam12split_2 PN:bam12split CL:/software/solexa/pkg/biobambam/2.0.43/bin/bam12split verbose=0 level=0 PP:samtools_2 VN:2.0.43 @PG ID:bamsormadup_2 PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsormadup threads=16 SO=queryname level=0 PP:bam12split_2 VN:2.0.43 @PG ID:AlignmentFilter_2 PN:AlignmentFilter CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_19727_3#11.bam, /tmp/tWRPF9NH3u/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/WcUu03_VA1/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=19727_3#11.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:bamsormadup_2 DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file VN:V1.19 @PG ID:bamsort_2 PN:bamsort CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane3/bsfopt_19727_3#11.tmp PP:AlignmentFilter_2 VN:2.0.43 @PG ID:bamstreamingmarkduplicates_2 PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane3/bmdfopt_19727_3#11.tmp M=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane3/19727_3#11.markdups_metrics.txt PP:bamsort_2 VN:2.0.43 @PG ID:scramble.1_2 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -t 7 -7 -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa PP:bamstreamingmarkduplicates_2 VN:1.14.8 @PG ID:SCS_3 PN:HiSeq Control Software PP:scramble.1_2 DS:Controlling software on instrument VN:2.2.68 @PG ID:basecalling_3 PN:RTA PP:SCS_3 DS:Basecalling Package VN:1.18.66.3 @PG ID:Illumina2bam_3 PN:Illumina2bam CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities BASECALLS_DIR=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BaseCalls LANE=4 OUTPUT=/dev/stdout READ_GROUP_ID=19727_4 SAMPLE_ALIAS=EGAN00001402033,EGAN00001402034,EGAN00001402035,EGAN00001402036,EGAN00001402037,EGAN00001402038,EGAN00001402039,EGAN00001402040,EGAN00001402041,EGAN00001402042,EGAN00001402043,EGAN00001402044,EGAN00001402045,EGAN00001402046,EGAN00001402047,EGAN00001402048,EGAN00001402049,EGAN00001402050,EGAN00001402051,EGAN00001402052,EGAN00001402053,EGAN00001402054,EGAN00001402055,EGAN00001402056 STUDY_NAME=EGAS00001001713: The Prenatal Assessment of Genomes and Exomes (PAGE) study is a multicentre prospective trial, performing exome sequence analysis on samples from 1000 families with structural anomalies in prenatal ultrasound screening but normal aneuploidy results. The data will enable discovery of novel genetic disorders and increase the diagnostic yield. Where appropriate, results will be reported back to the families at the end of the pregnancy, after thorough clinical review. Ultimately, the translation of the acquired know-how into cost-effective prenatal diagnostic sequencing will improve genetics-derived prognoses and allow more informed parental counselling as well as management of pregnancy and childbirth. PLATFORM_UNIT=160515_HS36_19727_A_C7FVUANXX_4 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT ADD_CLUSTER_INDEX_TAG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:basecalling_3 DS:Convert Illumina BCL to BAM or SAM file VN:V1.19 @PG ID:bamadapterfind_3 PN:bamadapterfind CL:bamadapterfind level=0 PP:Illumina2bam_3 VN:2.0.43 @PG ID:BamIndexDecoder_3 PN:BamIndexDecoder CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/metadata_cache_19727/lane_4.taglist METRICS_FILE=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/19727_4.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=false BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false CHANGE_READ_NAME=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bamadapterfind_3 DS:A command-line tool to decode multiplexed bam file VN:V1.19 @PG ID:spf_3 PN:spatial_filter CL:/software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -c -F pb_align_19727_4.bam.filter -t /nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/qc/tileviz/19727_4 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_19727_4.bam ; /software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -a -f -u -F pb_align_19727_4.bam.filter - PP:BamIndexDecoder_3 DS:A program to apply a spatial filter VN:v10.26-dirty @PG ID:bwa_3 PN:bwa PP:spf_3 VN:0.5.10-tpx @PG ID:BamMerger_3 PN:BamMerger CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_19727_4.bam INPUT=/dev/stdin OUTPUT=19727_4.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:bwa_3 DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.19 @PG ID:SplitBamByReadGroup_3 PN:SplitBamByReadGroup CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/19727_4.bam OUTPUT_PREFIX=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/lane4/ VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false PP:BamMerger_3 DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.19 @PG ID:bamcollate2_3 PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamcollate2 collate=1 level=0 PP:SplitBamByReadGroup_3 VN:2.0.43 @PG ID:bamreset_3 PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamreset resetaux=0 level=0 verbose=0 PP:bamcollate2_3 VN:2.0.43 @PG ID:bamadapterclip_3 PN:bamadapterclip CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamadapterclip verbose=0 level=0 PP:bamreset_3 VN:2.0.43 @PG ID:bwa'_3 PN:bwa CL:/software/solexa/pkg/bwa/0.7.13/bwa mem -t 16 -p -T 0 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/Cco9Jil7Dk/alntgt_bamtofastq_out PP:bamadapterclip_3 VN:0.7.13-r1126 @PG ID:scramble_3 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam PP:bwa'_3 VN:1.14.8 @PG ID:samtools_3 PN:samtools CL:/software/solexa/pkg/samtools/1.3.1-npg-Apr2016/bin/samtools reheader /tmp/j8Z7n6LIMx/postalntgt_alterSQ_headerSQfix_out /tmp/6dfCbI_8Rx/postalntgt_mbuffer_headerSQfix_out PP:scramble_3 VN:1.3.1-npg-Apr2016 @PG ID:bam12split_3 PN:bam12split CL:/software/solexa/pkg/biobambam/2.0.43/bin/bam12split verbose=0 level=0 PP:samtools_3 VN:2.0.43 @PG ID:bamsormadup_3 PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsormadup threads=16 SO=queryname level=0 PP:bam12split_3 VN:2.0.43 @PG ID:AlignmentFilter_3 PN:AlignmentFilter CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_19727_4#11.bam, /tmp/RWrgJhNxN3/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/Ktg_HxvQmz/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=19727_4#11.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false PP:bamsormadup_3 DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file VN:V1.19 @PG ID:bamsort_3 PN:bamsort CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane4/bsfopt_19727_4#11.tmp PP:AlignmentFilter_3 VN:2.0.43 @PG ID:bamstreamingmarkduplicates_3 PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane4/bmdfopt_19727_4#11.tmp M=/nfs/sf31/ILorHSany_sf31/outgoing/160515_HS36_19727_A_C7FVUANXX/Data/Intensities/BAM_basecalls_20160524-171745/no_cal/archive/lane4/19727_4#11.markdups_metrics.txt PP:bamsort_3 VN:2.0.43 @PG ID:scramble.1_3 PN:scramble CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -t 7 -7 -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa PP:bamstreamingmarkduplicates_3 VN:1.14.8 @PG ID:bammerge PN:bammerge CL:/software/solexa/pkg/biobambam/2.0.43/bin/bammerge level=0 SO=coordinate inputformat=cram outputformat=bam irods://irods-seq-sr01.internal.sanger.ac.uk/seq/19727/19727_1#11.cram irods://irods-seq-sr01.internal.sanger.ac.uk/seq/19727/19727_2#11.cram irods://irods-seq-sr01.internal.sanger.ac.uk/seq/19727/19727_3#11.cram irods://irods-seq-sr03.internal.sanger.ac.uk/seq/19727/19727_4#11.cram PP:scramble.1_3 VN:2.0.43 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.43/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=outdata/merge_bmd_16416685.ANXX.paired158.42e8dd0a3c.tmp M=outdata/16416685.ANXX.paired158.42e8dd0a3c.markdups_metrics.txt resetdupflag=1 PP:bammerge VN:2.0.43 @PG ID:scramble PN:scramble PP:bamstreamingmarkduplicates VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -7 -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:1 LN:249250621 AS:NCBI37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:2 LN:243199373 AS:NCBI37 M5:a0d9851da00400dec1098a9255ac712e SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:3 LN:198022430 AS:NCBI37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:4 LN:191154276 AS:NCBI37 M5:23dccd106897542ad87d2765d28a19a1 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:5 LN:180915260 AS:NCBI37 M5:0740173db9ffd264d728f32784845cd7 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:6 LN:171115067 AS:NCBI37 M5:1d3a93a248d92a729ee764823acbbc6b SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:7 LN:159138663 AS:NCBI37 M5:618366e953d6aaad97dbe4777c29375e SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:8 LN:146364022 AS:NCBI37 M5:96f514a9929e410c6651697bded59aec SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:9 LN:141213431 AS:NCBI37 M5:3e273117f15e0a400f01055d9f393768 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:10 LN:135534747 AS:NCBI37 M5:988c28e000e84c26d552359af1ea2e1d SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:11 LN:135006516 AS:NCBI37 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:12 LN:133851895 AS:NCBI37 M5:51851ac0e1a115847ad36449b0015864 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:13 LN:115169878 AS:NCBI37 M5:283f8d7892baa81b510a015719ca7b0b SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:14 LN:107349540 AS:NCBI37 M5:98f3cae32b2a2e9524bc19813927542e SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:15 LN:102531392 AS:NCBI37 M5:e5645a794a8238215b2cd77acb95a078 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:16 LN:90354753 AS:NCBI37 M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:17 LN:81195210 AS:NCBI37 M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:18 LN:78077248 AS:NCBI37 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:19 LN:59128983 AS:NCBI37 M5:1aacd71f30db8e561810913e0b72636d SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:20 LN:63025520 AS:NCBI37 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:21 LN:48129895 AS:NCBI37 M5:2979a6085bfe28e3ad6f552f361ed74d SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:22 LN:51304566 AS:NCBI37 M5:a718acaa6135fdca8357d5bfe94211dd SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:X LN:155270560 AS:NCBI37 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:Y LN:59373566 AS:NCBI37 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:MT LN:16569 AS:NCBI37 M5:c68f52674c9fb33aef52dcf399755519 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000207.1 LN:4262 AS:NCBI37 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000226.1 LN:15008 AS:NCBI37 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000229.1 LN:19913 AS:NCBI37 M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000231.1 LN:27386 AS:NCBI37 M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000210.1 LN:27682 AS:NCBI37 M5:851106a74238044126131ce2a8e5847c SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000239.1 LN:33824 AS:NCBI37 M5:99795f15702caec4fa1c4e15f8a29c07 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000235.1 LN:34474 AS:NCBI37 M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000201.1 LN:36148 AS:NCBI37 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000247.1 LN:36422 AS:NCBI37 M5:7de00226bb7df1c57276ca6baabafd15 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000245.1 LN:36651 AS:NCBI37 M5:89bc61960f37d94abf0df2d481ada0ec SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000197.1 LN:37175 AS:NCBI37 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000203.1 LN:37498 AS:NCBI37 M5:96358c325fe0e70bee73436e8bb14dbd SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000246.1 LN:38154 AS:NCBI37 M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000249.1 LN:38502 AS:NCBI37 M5:1d78abec37c15fe29a275eb08d5af236 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000196.1 LN:38914 AS:NCBI37 M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000248.1 LN:39786 AS:NCBI37 M5:5a8e43bec9be36c7b49c84d585107776 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000244.1 LN:39929 AS:NCBI37 M5:0996b4475f353ca98bacb756ac479140 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000238.1 LN:39939 AS:NCBI37 M5:131b1efc3270cc838686b54e7c34b17b SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000202.1 LN:40103 AS:NCBI37 M5:06cbf126247d89664a4faebad130fe9c SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000234.1 LN:40531 AS:NCBI37 M5:93f998536b61a56fd0ff47322a911d4b SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000232.1 LN:40652 AS:NCBI37 M5:3e06b6741061ad93a8587531307057d8 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000206.1 LN:41001 AS:NCBI37 M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000240.1 LN:41933 AS:NCBI37 M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000236.1 LN:41934 AS:NCBI37 M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000241.1 LN:42152 AS:NCBI37 M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000243.1 LN:43341 AS:NCBI37 M5:cc34279a7e353136741c9fce79bc4396 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000242.1 LN:43523 AS:NCBI37 M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000230.1 LN:43691 AS:NCBI37 M5:b4eb71ee878d3706246b7c1dbef69299 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000237.1 LN:45867 AS:NCBI37 M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000233.1 LN:45941 AS:NCBI37 M5:7fed60298a8d62ff808b74b6ce820001 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000204.1 LN:81310 AS:NCBI37 M5:efc49c871536fa8d79cb0a06fa739722 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000198.1 LN:90085 AS:NCBI37 M5:868e7784040da90d900d2d1b667a1383 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000208.1 LN:92689 AS:NCBI37 M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000191.1 LN:106433 AS:NCBI37 M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000227.1 LN:128374 AS:NCBI37 M5:a4aead23f8053f2655e468bcc6ecdceb SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000228.1 LN:129120 AS:NCBI37 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000214.1 LN:137718 AS:NCBI37 M5:46c2032c37f2ed899eb41c0473319a69 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000221.1 LN:155397 AS:NCBI37 M5:3238fb74ea87ae857f9c7508d315babb SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000209.1 LN:159169 AS:NCBI37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000218.1 LN:161147 AS:NCBI37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000220.1 LN:161802 AS:NCBI37 M5:fc35de963c57bf7648429e6454f1c9db SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000213.1 LN:164239 AS:NCBI37 M5:9d424fdcc98866650b58f004080a992a SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000211.1 LN:166566 AS:NCBI37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000199.1 LN:169874 AS:NCBI37 M5:569af3b73522fab4b40995ae4944e78e SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000217.1 LN:172149 AS:NCBI37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000216.1 LN:172294 AS:NCBI37 M5:642a232d91c486ac339263820aef7fe0 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000215.1 LN:172545 AS:NCBI37 M5:5eb3b418480ae67a997957c909375a73 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000205.1 LN:174588 AS:NCBI37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000219.1 LN:179198 AS:NCBI37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000224.1 LN:179693 AS:NCBI37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000223.1 LN:180455 AS:NCBI37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000195.1 LN:182896 AS:NCBI37 M5:5d9ec007868d517e73543b005ba48535 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000212.1 LN:186858 AS:NCBI37 M5:563531689f3dbd691331fd6c5730a88b SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000222.1 LN:186861 AS:NCBI37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000200.1 LN:187035 AS:NCBI37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000193.1 LN:189789 AS:NCBI37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000194.1 LN:191469 AS:NCBI37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000225.1 LN:211173 AS:NCBI37 M5:63945c3e6962f28ffd469719a747e73c SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:GL000192.1 LN:547496 AS:NCBI37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:NC_007605 LN:171823 AS:NCBI37 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @SQ SN:hs37d5 LN:35477943 AS:NCBI37 M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1 SP:Human UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa