@HD VN:1.4 SO:coordinate @RG ID:1#11 PL:ILLUMINA PU:140409_MS5_12602_A_MS2006456-150V3_1#11 LB:9857011 DS:EGAS00001000758: This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2014-04-09T00:00:00+0100 SM:EGAN00001195046 PG:BamIndexDecoder CN:SC @PG ID:SCS PN:MiSeq Control Software DS:Controlling software on instrument VN:2.3.0.3 @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.18.42.0 @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.13 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001195043,EGAN00001195044,EGAN00001195045,EGAN00001195046 STUDY_NAME=EGAS00001000758: This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ 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:0.0.129 CL:bamadapterfind level=0 @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.13 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/12602_1.bam BARCODE_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/lane_1.taglist METRICS_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/12602_1.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true 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:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamIndexDecoder 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:V1.13 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/12602_1.bam OUTPUT_PREFIX=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/lane1/12602_1 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/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa -b1 /nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/lane1/12602_1#11.bam > /tmp/epLrpXQvHX/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/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa -b2 /nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/lane1/12602_1#11.bam > /tmp/epLrpXQvHX/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/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/bwa/Homo_sapiens.GRCh37.dna.all.fa /tmp/epLrpXQvHX/1.sai /tmp/epLrpXQvHX/2.sai /nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/lane1/12602_1#11.bam /nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/lane1/12602_1#11.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 PN:BamMerger PP:samtools_fixmate 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:V1.13 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=/dev/stdin ALIGNMENT_PROGRAM_ID=NULL KEEP_ALL_PG=true INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/lane1/12602_1#11.bam OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/archive/lane1/12602_1#11.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:bamsort PN:bamsort PP:BamMerger VN:0.0.129 CL:/software/hpag/biobambam/0.0.129/bin/bamsort tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/archive/lane1/_IYxxFqpxA/ @PG ID:bammarkduplicates PN:bammarkduplicates PP:bamsort VN:0.0.129 CL:/software/hpag/biobambam/0.0.129/bin/bammarkduplicates I=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/archive/lane1/_IYxxFqpxA/sorted.bam O=/dev/stdout tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/archive/lane1/_IYxxFqpxA/ M=/tmp/GlrHMNjL2a level=0 @PG ID:BamTagStripper PN:BamTagStripper PP:bammarkduplicates 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:V1.13 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/sf49/ILorHSorMS_sf49/analysis/140409_MS5_12602_A_MS2006456-150V3/Data/Intensities/BAM_basecalls_20140410-084919/no_cal/archive/lane1/_IYxxFqpxA] 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:1.13.5 CL:/software/badger/bin/scramble -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa @SQ SN:Chr1 LN:249250621 UR:/lustre/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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 LN:19913 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG24 LN:27386 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Homo sapiens @SQ SN:HSCHR21_RANDOM_CTG9 LN:27682 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:851106a74238044126131ce2a8e5847c SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG32 LN:33824 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:99795f15702caec4fa1c4e15f8a29c07 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG28 LN:34474 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Homo sapiens @SQ SN:HSCHR9_RANDOM_CTG5 LN:36148 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG40 LN:36422 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:7de00226bb7df1c57276ca6baabafd15 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG38 LN:36651 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:89bc61960f37d94abf0df2d481ada0ec SP:Homo sapiens @SQ SN:HSCHR8_RANDOM_CTG4 LN:37175 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Homo sapiens @SQ SN:HSCHR17_RANDOM_CTG1 LN:37498 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:96358c325fe0e70bee73436e8bb14dbd SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG39 LN:38154 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG42 LN:38502 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:1d78abec37c15fe29a275eb08d5af236 SP:Homo sapiens @SQ SN:HSCHR8_RANDOM_CTG1 LN:38914 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG41 LN:39786 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:5a8e43bec9be36c7b49c84d585107776 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG37 LN:39929 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:0996b4475f353ca98bacb756ac479140 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG31 LN:39939 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:131b1efc3270cc838686b54e7c34b17b SP:Homo sapiens @SQ SN:HSCHR11_RANDOM_CTG2 LN:40103 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:06cbf126247d89664a4faebad130fe9c SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG27 LN:40531 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:93f998536b61a56fd0ff47322a911d4b SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG25 LN:40652 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:3e06b6741061ad93a8587531307057d8 SP:Homo sapiens @SQ SN:HSCHR17_RANDOM_CTG4 LN:41001 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG33 LN:41933 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG29 LN:41934 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG34 LN:42152 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG36 LN:43341 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:cc34279a7e353136741c9fce79bc4396 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG35 LN:43523 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG23 LN:43691 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:b4eb71ee878d3706246b7c1dbef69299 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG30 LN:45867 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG26 LN:45941 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:7fed60298a8d62ff808b74b6ce820001 SP:Homo sapiens @SQ SN:HSCHR17_RANDOM_CTG2 LN:81310 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:efc49c871536fa8d79cb0a06fa739722 SP:Homo sapiens @SQ SN:HSCHR9_RANDOM_CTG1 LN:90085 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:868e7784040da90d900d2d1b667a1383 SP:Homo sapiens @SQ SN:HSCHR19_RANDOM_CTG1 LN:92689 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Homo sapiens @SQ SN:HSCHR1_RANDOM_CTG5 LN:106433 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG20 LN:128374 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:a4aead23f8053f2655e468bcc6ecdceb SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG21 LN:129120 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG4 LN:137718 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:46c2032c37f2ed899eb41c0473319a69 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG13 LN:155397 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:3238fb74ea87ae857f9c7508d315babb SP:Homo sapiens @SQ SN:HSCHR19_RANDOM_CTG2 LN:159169 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG9 LN:161147 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:1d708b54644c26c7e01c2dad5426d38c SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG11 LN:161802 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:fc35de963c57bf7648429e6454f1c9db SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG3 LN:164239 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:9d424fdcc98866650b58f004080a992a SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG1 LN:166566 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo sapiens @SQ SN:HSCHR9_RANDOM_CTG2 LN:169874 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:569af3b73522fab4b40995ae4944e78e SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG7 LN:172149 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:6d243e18dea1945fb7f2517615b8f52e SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG6 LN:172294 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:642a232d91c486ac339263820aef7fe0 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG5 LN:172545 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:5eb3b418480ae67a997957c909375a73 SP:Homo sapiens @SQ SN:HSCHR17_RANDOM_CTG3 LN:174588 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:d22441398d99caf673e9afb9a1908ec5 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG10 LN:179198 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG16 LN:179693 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG15 LN:180455 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo sapiens @SQ SN:HSCHR7_RANDOM_CTG1 LN:182896 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:5d9ec007868d517e73543b005ba48535 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG2 LN:186858 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:563531689f3dbd691331fd6c5730a88b SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG14 LN:186861 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Homo sapiens @SQ SN:HSCHR9_RANDOM_CTG4 LN:187035 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Homo sapiens @SQ SN:HSCHR4_RANDOM_CTG2 LN:189789 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo sapiens @SQ SN:HSCHR4_RANDOM_CTG3 LN:191469 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo sapiens @SQ SN:HSCHRUN_RANDOM_CTG17 LN:211173 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:63945c3e6962f28ffd469719a747e73c SP:Homo sapiens @SQ SN:HSCHR1_RANDOM_CTG12 LN:547496 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/GRCh37_53/all/fasta/Homo_sapiens.GRCh37.dna.all.fa AS:GRCh37 53 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo sapiens