@HD VN:1.4 SO:coordinate @RG ID:1#8 PL:ILLUMINA PU:140428_HS27_12736_A_C3880ACXX_4#8 LB:9980418 DS:Pilot experiment on functional genomics in osteoarthritis_RNA: The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data. DT:2014-04-28T00:00:00+0100 SM:SMBP054D PG:BamIndexDecoder CN:SC @PG ID:SCS PN:HiSeq Control Software DS:Controlling software on instrument VN:2.0.12.0 @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.21.3 @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/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities BASECALLS_DIR=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BaseCalls LANE=4 OUTPUT=/dev/stdout SAMPLE_ALIAS=SMBP049C,SMBP049D,SMBP051C,SMBP051D,SMBP053C,SMBP053D,SMBP054C,SMBP054D,SMBP055C,SMBP055D,SMBP056C,SMBP056D,SMBP059C,SMBP059D,SMBP060C,SMBP060D,SMBP061C,SMBP061D,SMBP064C,SMBP064D,SMBP065C,SMBP065D,SMBP066C,SMBP066D,phiX_for_spiked_buffers STUDY_NAME=Pilot experiment on functional genomics in osteoarthritis_RNA: The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.,Illumina Controls: SPIKED_CONTROL 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/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/12736_4.bam BARCODE_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/lane_4.taglist METRICS_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/12736_4.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:spf PN:spatial_filter PP:BamIndexDecoder DS:A program to apply a spatial filter VN:v10.14 CL:/software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -c -F pb_align_12736_4.bam.filter -t /nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/qc/tileviz/12736_4 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_12736_4.bam ; /software/solexa/pkg/pb_calibration/v10.14/bin/spatial_filter -a -u -F pb_align_12736_4.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:V1.13 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_12736_4.bam INPUT=/dev/stdin OUTPUT=12736_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 @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:V1.13 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/12736_4.bam OUTPUT_PREFIX=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/lane4/12736_4 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/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/lane4/12736_4#8.bam > /tmp/eRbX30M91L/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/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/lane4/12736_4#8.bam > /tmp/eRbX30M91L/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/eRbX30M91L/1.sai /tmp/eRbX30M91L/2.sai /nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/lane4/12736_4#8.bam /nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/lane4/12736_4#8.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:V1.13 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/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/lane4/12736_4#8.bam OUTPUT=/tmp/eRbX30M91L/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:V1.13 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/lane4/12736_4#8.bam, /tmp/eRbX30M91L/output_fifo.bam] OUTPUT_ALIGNMENT=[/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/lane4/12736_4#8_phix.bam, /nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/lane4/12736_4#8.bam] METRICS_FILE=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/lane4/12736_4#8.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:0.0.129 CL:/software/hpag/biobambam/0.0.129/bin/bamsort tmpfile=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/lane4/xOHnnvoyfx/ @PG ID:bammarkduplicates PN:bammarkduplicates PP:bamsort VN:0.0.129 CL:/software/hpag/biobambam/0.0.129/bin/bammarkduplicates I=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/lane4/xOHnnvoyfx/sorted.bam O=/dev/stdout tmpfile=/nfs/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/lane4/xOHnnvoyfx/ M=/tmp/iRTUx0jPC6 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/sf32/ILorHSany_sf32/analysis/140428_HS27_12736_A_C3880ACXX/Data/Intensities/BAM_basecalls_20140505-120920/no_cal/archive/lane4/xOHnnvoyfx] 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 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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 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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 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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