@HD VN:1.4 SO:coordinate @RG ID:1#49 PL:ILLUMINA PU:150203_HS34_15415_A_HB1H6ADXX_2#49 LB:12906355 DS:Single Cell Methods - DNARNA: This study aims to further develop methods for combined sequencing of DNA and RNA from single cells. DT:2015-02-03T00:00:00+0000 SM:HCC38_1_GT_10 PG:BamIndexDecoder CN:SC @PG ID:SCS PN:HiSeq Control Software DS:Controlling software on instrument VN:2.2.38 @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.18.61.0 @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.16 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities BASECALLS_DIR=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BaseCalls LANE=2 OUTPUT=/dev/stdout SAMPLE_ALIAS=HCC38_20_GT_1,HCC38_10_GT_1,HCC38_5_GT_1,HCC38BL_20_GT_1,HCC38BL_10_GT_1,HCC38BL_5_GT_1,HCC38_20_SS2_1,HCC38_10_SS2_1,HCC38_5_SS2_1,HCC38BL_20_SS2_1,HCC38BL_10_SS2_1,HCC38BL_5_SS2_1,HCC38_1_GT_1,HCC38_1_GT_2,HCC38_1_GT_3,HCC38BL_1_GT_1,HCC38BL_1_GT_2,HCC38BL_1_GT_3,HCC38_1_SS2_1,HCC38_1_SS2_2,HCC38_1_SS2_3,HCC38BL_1_SS2_1,HCC38BL_1_SS2_2,HCC38BL_1_SS2_3,HCC38_1_GT_4,HCC38_1_GT_5,HCC38_1_GT_6,HCC38BL_1_GT_4,HCC38BL_1_GT_5,HCC38BL_1_GT_6,HCC38_1_SS2_4,HCC38_1_SS2_5,HCC38_1_SS2_6,HCC38BL_1_SS2_4,HCC38BL_1_SS2_5,HCC38BL_1_SS2_6,HCC38_1_GT_7,HCC38_1_GT_8,HCC38_1_GT_9,HCC38BL_1_GT_7,HCC38BL_1_GT_8,HCC38BL_1_GT_9,HCC38_1_SS2_7,HCC38_1_SS2_8,HCC38_1_SS2_9,HCC38BL_1_SS2_7,HCC38BL_1_SS2_8,HCC38BL_1_SS2_9,HCC38_1_GT_10,HCC38_1_GT_11,HCC38_1_GT_12,HCC38BL_1_GT_10,HCC38BL_1_GT_11,HCC38BL_1_GT_12,HCC38_1_SS2_10,HCC38_1_SS2_11,HCC38_1_SS2_12,HCC38BL_1_SS2_10,HCC38BL_1_SS2_11,HCC38BL_1_SS2_12,HCC38_1_GT_13,HCC38_1_GT_14,HCC38_1_GT_15,HCC38BL_1_GT_13,HCC38BL_1_GT_14,HCC38BL_1_GT_15,HCC38_1_SS2_13,HCC38_1_SS2_14,HCC38_1_SS2_15,HCC38BL_1_SS2_13,HCC38BL_1_SS2_14,HCC38BL_1_SS2_15,HCC38_1_GT_16,HCC38_1_GT_17,HCC38_1_GT_18,HCC38BL_1_GT_16,HCC38BL_1_GT_17,HCC38BL_1_GT_18,HCC38_1_SS2_16,HCC38_1_SS2_17,HCC38_1_SS2_18,HCC38BL_1_SS2_16,HCC38BL_1_SS2_17,HCC38BL_1_SS2_18,HCC38_1_GT_19,HCC38_1_GT_20,HCC38_0_GT_1,HCC38BL_1_GT_19,HCC38BL_1_GT_20,HCC38BL_0_GT_1,HCC38_1_SS2_19,HCC38_1_SS2_20,HCC38_0_SS2_1,HCC38BL_1_SS2_19,HCC38BL_1_SS2_20,HCC38BL_0_SS2_1 STUDY_NAME=Single Cell Methods - DNARNA: This study aims to further develop methods for combined sequencing of DNA and RNA from single cells. PLATFORM_UNIT=150203_HS34_15415_A_HB1H6ADXX_2 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT 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:0.0.180 CL:bamadapterfind level=0 @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.16 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/metadata_cache_15415/lane_2.taglist METRICS_FILE=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/15415_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 MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:spf PN:spatial_filter PP:BamIndexDecoder DS:A program to apply a spatial filter VN:v10.21 CL:/software/solexa/pkg/pb_calibration/v10.21/bin/spatial_filter -c -F pb_align_15415_2.bam.filter -t /nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/qc/tileviz/15415_2 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_15415_2.bam ; /software/solexa/pkg/pb_calibration/v10.21/bin/spatial_filter -a -f -u -F pb_align_15415_2.bam.filter - @PG ID:bwa PN:bwa PP:spf VN:0.5.10-tpx @PG ID:BamMerger PN:BamMerger PP:bwa 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:V1.16 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_15415_2.bam INPUT=/dev/stdin OUTPUT=15415_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 @PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger 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:V1.16 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/15415_2.bam OUTPUT_PREFIX=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/lane2/15415_2 OUTPUT_COMMON_RG_HEAD_TO_TRIM=1 VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:bwa_aln PN:bwa PP:SplitBamByReadGroup VN:0.5.10-tpx CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa aln -q 15 -t 12 /lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa -b1 /nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/lane2/15415_2#49.bam > /tmp/UOidwD5UC0/1.sai @PG ID:bwa_aln_1 PN:bwa PP:bwa_aln VN:0.5.10-tpx CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa aln -q 15 -t 12 /lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa -b2 /nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/lane2/15415_2#49.bam > /tmp/UOidwD5UC0/2.sai @PG ID:bwa_sam PN:bwa PP:bwa_aln_1 VN:0.5.10-tpx CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa sampe -t 6 /lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa /tmp/UOidwD5UC0/1.sai /tmp/UOidwD5UC0/2.sai /nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/lane2/15415_2#49.bam /nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/lane2/15415_2#49.bam @PG ID:Picard_SamFormatConverter PN:SamFormatConverter PP:bwa_sam VN:1.72(1230) CL:/software/jdk1.7.0_25/bin/java -Xmx1000m -jar /software/solexa/pkg/picard/picard-tools-1.72/SamFormatConverter.jar VALIDATION_STRINGENCY=SILENT INPUT=/dev/stdin OUTPUT=/dev/stdout COMPRESSION_LEVEL=0 @PG ID:samtools_fixmate PN:samtools PP:Picard_SamFormatConverter VN:0.1.18 (r982:295) CL:/software/solexa/pkg/samtools/samtools-0.1.18/samtools fixmate - - @PG ID:BamMerger_1 PN:BamMerger PP:samtools_fixmate VN:V1.16 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 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=/dev/stdin ALIGNMENT_PROGRAM_ID=NULL KEEP_ALL_PG=true INPUT=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/lane2/15415_2#49.bam OUTPUT=/tmp/UOidwD5UC0/output_fifo.bam KEEP_EXTRA_UNMAPPED_READS=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true REPLACE_ALIGNED_BASE_QUALITY=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:AlignmentFilter PN:AlignmentFilter PP:BamMerger_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:V1.16 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/lane2/15415_2#49.bam, /tmp/UOidwD5UC0/output_fifo.bam] OUTPUT_ALIGNMENT=[/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/lane2/15415_2#49_phix.bam, /nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/lane2/15415_2#49.bam] METRICS_FILE=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/lane2/15415_2#49.bam_alignment_filter_metrics.json VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:bamsort PN:bamsort PP:AlignmentFilter VN:0.0.180 CL:/software/hpag/biobambam/0.0.180/bin/bamsort tmpfile=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/lane2/ePeyuCgZXJ/ @PG ID:bammarkduplicates2 PN:bammarkduplicates2 PP:bamsort VN:0.0.180 CL:/software/hpag/biobambam/0.0.180/bin/bammarkduplicates2 I=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/lane2/ePeyuCgZXJ/sorted.bam O=/dev/stdout tmpfile=/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/lane2/ePeyuCgZXJ/ M=/tmp/EuMFkYW9ZA level=0 @PG ID:BamTagStripper PN:BamTagStripper PP:bammarkduplicates2 DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.16 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/dev/stdout TAG_TO_KEEP=[a3, aa, af, ah, as, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf43/ILorHSany_sf43/analysis/150203_HS34_15415_A_HB1H6ADXX/Data/Intensities/BAM_basecalls_20150204-144947/no_cal/archive/lane2/ePeyuCgZXJ] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=false CREATE_MD5_FILE=false QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 @PG ID:scramble PN:scramble PP:BamTagStripper VN:1.13.8 CL:/software/solexa/bin/scramble -I bam -O cram -r /lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa @SQ SN:Chr1 LN:249250621 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo sapiens @SQ SN:Chr2 LN:243199373 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:a0d9851da00400dec1098a9255ac712e SP:Homo sapiens @SQ SN:Chr3 LN:198022430 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo sapiens @SQ SN:Chr4 LN:191154276 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:23dccd106897542ad87d2765d28a19a1 SP:Homo sapiens @SQ SN:Chr5 LN:180915260 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:0740173db9ffd264d728f32784845cd7 SP:Homo sapiens @SQ SN:Chr6 LN:171115067 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo sapiens @SQ SN:Chr7 LN:159138663 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:618366e953d6aaad97dbe4777c29375e SP:Homo sapiens @SQ SN:Chr8 LN:146364022 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:96f514a9929e410c6651697bded59aec SP:Homo sapiens @SQ SN:Chr9 LN:141213431 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:3e273117f15e0a400f01055d9f393768 SP:Homo sapiens @SQ SN:Chr10 LN:135534747 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:988c28e000e84c26d552359af1ea2e1d SP:Homo sapiens @SQ SN:Chr11 LN:135006516 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo sapiens @SQ SN:Chr12 LN:133851895 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:51851ac0e1a115847ad36449b0015864 SP:Homo sapiens @SQ SN:Chr13 LN:115169878 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:283f8d7892baa81b510a015719ca7b0b SP:Homo sapiens @SQ SN:Chr14 LN:107349540 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:98f3cae32b2a2e9524bc19813927542e SP:Homo sapiens @SQ SN:Chr15 LN:102531392 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:e5645a794a8238215b2cd77acb95a078 SP:Homo sapiens @SQ SN:Chr16 LN:90354753 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo sapiens @SQ SN:Chr17 LN:81195210 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo sapiens @SQ SN:Chr18 LN:78077248 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo sapiens @SQ SN:Chr19 LN:59128983 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:1aacd71f30db8e561810913e0b72636d SP:Homo sapiens @SQ SN:Chr20 LN:63025520 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo sapiens @SQ SN:Chr21 LN:48129895 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo sapiens @SQ SN:Chr22 LN:51304566 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo sapiens @SQ SN:ChrX LN:155270560 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo sapiens @SQ SN:ChrY LN:59373566 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Homo sapiens @SQ SN:HSCHR18_RANDOM_CTG1 LN:4262 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG19 LN:15008 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG22 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