@HD VN:1.4 SO:coordinate @RG ID:20788_8#1 PL:ILLUMINA PU:160914_HX3_20788_A_HWFLFCCXX_8#1 LB:17599338 DS:EGAS00001001355: Whole genome sequencing of participants from the INTERVAL study. DT:2016-09-14T00:00:00+0100 SM:EGAN00001435500 PG:BamIndexDecoder CN:SC @PG ID:SCS PN:HiSeq Control Software DS:Controlling software on instrument VN:3.3.76 @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:2.7.6 @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.19 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities BASECALLS_DIR=/nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BaseCalls LANE=8 OUTPUT=/dev/stdout READ_GROUP_ID=20788_8 SAMPLE_ALIAS=EGAN00001435500,EGAN00001436553,EGAN00001247692,EGAN00001241988,EGAN00001242162,EGAN00001242412,EGAN00001242982,EGAN00001243613,EGAN00001243716,EGAN00001244035,EGAN00001244189,EGAN00001244491 STUDY_NAME="EGAS00001001355: Whole genome sequencing of participants from the INTERVAL study." PLATFORM_UNIT=160914_HX3_20788_A_HWFLFCCXX_8 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 @PG ID:bamadapterfind PN:bamadapterfind PP:Illumina2bam VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamadapterfind level=0 @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.19 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/metadata_cache_20788/lane_8.taglist METRICS_FILE=/nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/20788_8.bam.tag_decode.metrics 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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:bamcollate2 PN:bamcollate2 PP:BamIndexDecoder VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamcollate2 collate=2 level=0 @PG ID:bwa PN:bwa PP:bamcollate2 VN:0.7.13-r1126 CL:/software/solexa/pkg/bwa/0.7.13/bwa sampe /lustre/scratch110/srpipe/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/qRJ03DfEfz/alnphix_bwa_aln_1_out /tmp/9XVD9BpnL8/alnphix_bwa_aln_2_out /tmp/OHeL343r1b/alnphix_simple_cat1_out /tmp/s8wMbGiCnt/alnphix_simple_cat2_out @PG ID:scramble PN:scramble PP:bwa VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -t 1 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/SnMDKtivGR/simple_cat_out @PG ID:scramble.1 PN:scramble PP:bam12auxmerge VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -I bam -O cram -x -3 @PG ID:scramble.2 PN:scramble PP:scramble.1 VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -I cram -O bam -0 @PG ID:spf PN:spatial_filter PP:scramble.2 DS:A program to apply a spatial filter VN:v10.26-dirty CL:/software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/no_cal/archive/qc/tileviz/20788_8 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 /dev/stdin ; /software/solexa/pkg/pb_calibration/10.26/bin/spatial_filter -a -f -u -l /nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/no_cal/20788_8.bam.filter.stats -F /tmp/WKavQq2pb8/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.3.1-npg-May2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-May2016/bin/samtools split -f /nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/no_cal/lane8/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 PP:samtools VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2' VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamadapterclip verbose=0 level=0 @PG ID:bwa' PN:bwa PP:bamadapterclip VN:0.7.13-r1126 CL:/software/solexa/pkg/bwa/0.7.13/bwa mem -t 16 -p -T 0 /lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/bwa0_6/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa /tmp/BEUmqMYIiv/alntgt_bamtofastq_out @PG ID:scramble' PN:scramble PP:bwa' VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam @PG ID:samtools' PN:samtools PP:scramble' VN:1.3.1-npg-May2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-May2016/bin/samtools reheader /tmp/2SOtMCAJBA/postalntgt_alterSQ_headerSQfix_out /tmp/OxAIBwdSHg/postalntgt_mbuffer_headerSQfix_out @PG ID:bam12split PN:bam12split PP:samtools' VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bam12split verbose=0 level=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamsormadup threads=16 SO=queryname level=0 @PG ID:bam12auxmerge' PN:bam12auxmerge PP:bamsormadup VN:2.0.50 CL:/software/solexa/pkg/biobambam/2.0.50/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/7ScfL3uao7/amp_bamadapterclip_pre_auxmerge_out @PG ID:AlignmentFilter PN:AlignmentFilter PP:bam12auxmerge' 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 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_20788_8#1.bam, /tmp/Y699j3fMqR/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/sxmABOBLAo/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=20788_8#1.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 @PG ID:bamsort PN:bamsort CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/no_cal/archive/lane8/bsfopt_20788_8#1.tmp PP:AlignmentFilter VN:2.0.50 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.50/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/no_cal/archive/lane8/bmdfopt_20788_8#1.tmp M=/nfs/sf20/ILorHSany_sf20/analysis/160914_HX3_20788_A_HWFLFCCXX/Data/Intensities/BAM_basecalls_20161003-140651/no_cal/archive/lane8/20788_8#1.markdups_metrics.txt PP:bamsort VN:2.0.50 @PG ID:scramble.3 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -t 7 -7 -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa @SQ SN:chr1 LN:248956422 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:6aef897c3d6ff0c78aff06ac189178dd SP:Human @SQ SN:chr2 LN:242193529 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:f98db672eb0993dcfdabafe2a882905c SP:Human @SQ SN:chr3 LN:198295559 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:76635a41ea913a405ded820447d067b0 SP:Human @SQ SN:chr4 LN:190214555 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:3210fecf1eb92d5489da4346b3fddc6e SP:Human @SQ SN:chr5 LN:181538259 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:a811b3dc9fe66af729dc0dddf7fa4f13 SP:Human @SQ SN:chr6 LN:170805979 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:5691468a67c7e7a7b5f2a3a683792c29 SP:Human @SQ SN:chr7 LN:159345973 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:cc044cc2256a1141212660fb07b6171e SP:Human @SQ SN:chr8 LN:145138636 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:c67955b5f7815a9a1edfaa15893d3616 SP:Human @SQ SN:chr9 LN:138394717 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:6c198acf68b5af7b9d676dfdd531b5de SP:Human @SQ SN:chr10 LN:133797422 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:c0eeee7acfdaf31b770a509bdaa6e51a SP:Human @SQ SN:chr11 LN:135086622 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:1511375dc2dd1b633af8cf439ae90cec SP:Human @SQ SN:chr12 LN:133275309 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:96e414eace405d8c27a6d35ba19df56f SP:Human @SQ SN:chr13 LN:114364328 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:a5437debe2ef9c9ef8f3ea2874ae1d82 SP:Human @SQ SN:chr14 LN:107043718 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:e0f0eecc3bcab6178c62b6211565c807 SP:Human @SQ SN:chr15 LN:101991189 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:f036bd11158407596ca6bf3581454706 SP:Human @SQ SN:chr16 LN:90338345 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:db2d37c8b7d019caaf2dd64ba3a6f33a SP:Human @SQ SN:chr17 LN:83257441 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:f9a0fb01553adb183568e3eb9d8626db SP:Human @SQ SN:chr18 LN:80373285 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:11eeaa801f6b0e2e36a1138616b8ee9a SP:Human @SQ SN:chr19 LN:58617616 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:85f9f4fc152c58cb7913c06d6b98573a SP:Human @SQ SN:chr20 LN:64444167 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:b18e6c531b0bd70e949a7fc20859cb01 SP:Human @SQ SN:chr21 LN:46709983 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:974dc7aec0b755b19f031418fdedf293 SP:Human @SQ SN:chr22 LN:50818468 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:ac37ec46683600f808cdd41eac1d55cd SP:Human @SQ SN:chrX LN:156040895 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:2b3a55ff7f58eb308420c8a9b11cac50 SP:Human @SQ SN:chrY LN:57227415 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:ce3e31103314a704255f3cd90369ecce SP:Human @SQ SN:chrM LN:16569 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:c68f52674c9fb33aef52dcf399755519 SP:Human @SQ SN:chr1_KI270706v1_random LN:175055 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:62def1a794b3e18192863d187af956e6 SP:Human @SQ SN:chr1_KI270707v1_random LN:32032 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:78135804eb15220565483b7cdd02f3be SP:Human @SQ SN:chr1_KI270708v1_random LN:127682 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:1e95e047b98ed92148dd84d6c037158c SP:Human @SQ SN:chr1_KI270709v1_random LN:66860 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:4e2db2933ea96aee8dab54af60ecb37d SP:Human @SQ 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