@HD VN:1.4 SO:coordinate @RG ID:1#24 PL:ILLUMINA PU:131105_MS2_11292_A_MS2033183-300V2_1#24 LB:8405268 DS:Breast Heterogeneity Validation: Validation of subs and indels called in breast whole genome studies DT:2013-11-05T00:00:00+0000 SM:2783STDY5606709 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:V1.12 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=2783STDY5606686,2783STDY5606687,2783STDY5606688,2783STDY5606689,2783STDY5606690,2783STDY5606691,2783STDY5606692,2783STDY5606693,2783STDY5606694,2783STDY5606695,2783STDY5606696,2783STDY5606697,2783STDY5606698,2783STDY5606699,2783STDY5606700,2783STDY5606701,2783STDY5606702,2783STDY5606703,2783STDY5606704,2783STDY5606705,2783STDY5606706,2783STDY5606707,2783STDY5606708,2783STDY5606709,2783STDY5606710,2783STDY5606711,2783STDY5606712,2783STDY5606713,2783STDY5606714,2783STDY5606715,2783STDY5606716,2783STDY5606717,2783STDY5606718,2783STDY5606719,2783STDY5606720,2783STDY5606721,2783STDY5606722,2783STDY5606723,2783STDY5606724,2783STDY5606725,2783STDY5606726,2783STDY5606727,2783STDY5606728,2783STDY5606729,2783STDY5606730,2783STDY5606731,2783STDY5606732,2783STDY5606733,2783STDY5606734,2783STDY5606735,2783STDY5606736,2783STDY5606737,2783STDY5606738,2783STDY5606739,2783STDY5606740,2783STDY5606741,2783STDY5606742,2783STDY5606743,2783STDY5606744,2783STDY5606745,2783STDY5606746,2783STDY5606747 LIBRARY_NAME=8363998 STUDY_NAME=Breast Heterogeneity Validation: Validation of subs and indels called in breast whole genome studies COMPRESSION_LEVEL=0 CREATE_MD5_FILE=true GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 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 @PG ID:BamAdapterFinder PN:BamAdapterFinder PP:Illumina2bam DS:Find short inserts by finding overlapping forward/reverse reads. Note position with a tag. VN:V1.12 CL:uk.ac.sanger.npg.picard.BamAdapterFinder INPUT=/dev/stdin OUTPUT=/dev/stdout ADAPTER_LENGTH_TAG=a3 ADAPTER_MATCH_TAG=ah VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 CREATE_MD5_FILE=true MIN_OVERLAP=32 PCT_MISMATCHES=10.0 ADAPTER_MATCH=12 VERBOSITY=INFO QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:BamAdapterFinder DS:A command-line tool to decode multiplexed bam file VN:V1.12 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/11292_1.bam BARCODE_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/lane_1.taglist METRICS_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/11292_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:V1.12 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/11292_1.bam OUTPUT_PREFIX=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/lane1/11292_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/bin/aligners/bwa/bwa-0.5.10-mt/bwa aln -t 12 /lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa -b1 /nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/lane1/11292_1#24.bam > /tmp/LzlhY4W2pu/1.sai @PG ID:bwa_aln_1 PN:bwa PP:bwa_aln VN:0.5.10-tpx CL:/software/solexa/bin/aligners/bwa/bwa-0.5.10-mt/bwa aln -t 12 /lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa -b2 /nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/lane1/11292_1#24.bam > /tmp/LzlhY4W2pu/2.sai @PG ID:bwa_sam PN:bwa PP:bwa_aln_1 VN:0.5.10-tpx CL:/software/solexa/bin/aligners/bwa/bwa-0.5.10-mt/bwa sampe -t 6 /lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa /tmp/LzlhY4W2pu/1.sai /tmp/LzlhY4W2pu/2.sai /nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/lane1/11292_1#24.bam /nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/lane1/11292_1#24.bam @PG ID:Picard_SamFormatConverter PN:SamFormatConverter PP:bwa_sam VN:1.72(1230) CL:/software/java/bin/java -Xmx1000m -jar /software/solexa/bin/aligners/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/bin/aligners/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:V1.12 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/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/lane1/11292_1#24.bam OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/archive/lane1/11292_1#24.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:0.0.87 CL:/software/hpag/biobambam/0.0.87/bin/bamsort tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/archive/lane1/A7qZe0DEAZ/ @PG ID:bammarkduplicates PN:bammarkduplicates PP:bamsort VN:0.0.87 CL:/software/hpag/biobambam/0.0.87/bin/bammarkduplicates I=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/archive/lane1/A7qZe0DEAZ/sorted.bam O=/dev/stdout tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/archive/lane1/A7qZe0DEAZ/ M=/tmp/fwqUXn24gS 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:V1.12 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/dev/stdout TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/131105_MS2_11292_A_MS2033183-300V2/Data/Intensities/BAM_basecalls_20131106-135013/no_cal/archive/lane1/A7qZe0DEAZ] 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:1.13.3 CL:/software/badger/bin/scramble -I bam -O cram -r /lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa @SQ SN:1 LN:249250621 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo sapiens @SQ SN:2 LN:243199373 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:a0d9851da00400dec1098a9255ac712e SP:Homo sapiens @SQ SN:3 LN:198022430 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo sapiens @SQ SN:4 LN:191154276 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:23dccd106897542ad87d2765d28a19a1 SP:Homo sapiens @SQ SN:5 LN:180915260 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:0740173db9ffd264d728f32784845cd7 SP:Homo sapiens @SQ SN:6 LN:171115067 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo sapiens @SQ SN:7 LN:159138663 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:618366e953d6aaad97dbe4777c29375e SP:Homo sapiens @SQ SN:8 LN:146364022 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:96f514a9929e410c6651697bded59aec SP:Homo sapiens @SQ SN:9 LN:141213431 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:3e273117f15e0a400f01055d9f393768 SP:Homo sapiens @SQ SN:10 LN:135534747 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:988c28e000e84c26d552359af1ea2e1d SP:Homo sapiens @SQ SN:11 LN:135006516 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo sapiens @SQ SN:12 LN:133851895 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:51851ac0e1a115847ad36449b0015864 SP:Homo sapiens @SQ SN:13 LN:115169878 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:283f8d7892baa81b510a015719ca7b0b SP:Homo sapiens @SQ SN:14 LN:107349540 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:98f3cae32b2a2e9524bc19813927542e SP:Homo sapiens @SQ SN:15 LN:102531392 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:e5645a794a8238215b2cd77acb95a078 SP:Homo sapiens @SQ SN:16 LN:90354753 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo sapiens @SQ SN:17 LN:81195210 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo sapiens @SQ SN:18 LN:78077248 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo sapiens @SQ SN:19 LN:59128983 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:1aacd71f30db8e561810913e0b72636d SP:Homo sapiens @SQ SN:20 LN:63025520 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo sapiens @SQ SN:21 LN:48129895 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo sapiens @SQ SN:22 LN:51304566 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo sapiens @SQ SN:X LN:155270560 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo sapiens @SQ SN:Y LN:59373566 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:1e86411d73e6f00a10590f976be01623 SP:Homo sapiens @SQ SN:MT LN:16569 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/fasta/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa AS:CGP GRCh37.NCBI.allchr_MT M5:c68f52674c9fb33aef52dcf399755519 SP:Homo sapiens