@HD VN:1.4 SO:coordinate @RG ID:1#44 PL:ILLUMINA PU:141013_HS9_14417_B_C5RH1ACXX_4#44 LB:11559292 DS:EGAS00001000103: Exome pulldown and SNP6 Affymetrix array of matched primary and metastatic colorectal cancer samples from 20 patients DT:2014-10-13T00:00:00+0100 SM:EGAN00001213963 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:V1.16 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities BASECALLS_DIR=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BaseCalls LANE=4 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001213963,EGAN00001213965,EGAN00001213967,EGAN00001213969,EGAN00001213972,EGAN00001213974,EGAN00001213976,EGAN00001213978 STUDY_NAME=EGAS00001000103: Exome pulldown and SNP6 Affymetrix array of matched primary and metastatic colorectal cancer samples from 20 patients PLATFORM_UNIT=141013_HS9_14417_B_C5RH1ACXX_4 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:0.0.171 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=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/14417_4.bam BARCODE_FILE=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/lane_4.taglist METRICS_FILE=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/14417_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:v10.21 CL:/software/solexa/pkg/pb_calibration/v10.21/bin/spatial_filter -c -F pb_align_14417_4.bam.filter -t /nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/qc/tileviz/14417_4 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_14417_4.bam ; /software/solexa/pkg/pb_calibration/v10.21/bin/spatial_filter -a -f -u -F pb_align_14417_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:V1.16 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_14417_4.bam INPUT=/dev/stdin OUTPUT=14417_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:V1.16 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/14417_4.bam OUTPUT_PREFIX=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/lane4/14417_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 -t 16 /lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa -b1 /nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/lane4/14417_4#44.bam > /tmp/LijJO2rdmb/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 -t 16 /lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa -b2 /nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/lane4/14417_4#44.bam > /tmp/LijJO2rdmb/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/CGP_GRCh37.NCBI.allchr_MT/all/bwa/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa /tmp/LijJO2rdmb/1.sai /tmp/LijJO2rdmb/2.sai /nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/lane4/14417_4#44.bam /nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/lane4/14417_4#44.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/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/lane4/14417_4#44.bam OUTPUT=/tmp/LijJO2rdmb/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/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/lane4/14417_4#44.bam, /tmp/LijJO2rdmb/output_fifo.bam] OUTPUT_ALIGNMENT=[/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/lane4/14417_4#44_phix.bam, /nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/lane4/14417_4#44.bam] METRICS_FILE=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/lane4/14417_4#44.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:0.0.171 CL:/software/hpag/biobambam/0.0.171/bin/bamsort tmpfile=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/lane4/O3bPHuz8I6/ @PG ID:bammarkduplicates2 PN:bammarkduplicates2 PP:bamsort VN:0.0.171 CL:/software/hpag/biobambam/0.0.171/bin/bammarkduplicates2 I=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/lane4/O3bPHuz8I6/sorted.bam O=/dev/stdout tmpfile=/nfs/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/lane4/O3bPHuz8I6/ M=/tmp/bL_HjDx2ZH 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/sf47/ILorHSany_sf47/analysis/141013_HS9_14417_B_C5RH1ACXX/Data/Intensities/BAM_basecalls_20141022-151933/no_cal/archive/lane4/O3bPHuz8I6] 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/solexa/bin/scramble -I bam -O cram -r /lustre/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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/scratch110/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