@HD VN:1.4 SO:coordinate @RG ID:21698_1#20 PL:ILLUMINA PU:170117_HS33_21698_A_CA42YANXX_1#20 LB:13958076 DS:EGAS00001000570: Genomic libraries will be generated from total genomic DNA derived from 4000 samples with Acute Myeloid Leukaemia. Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 64 Samples will be individually barcoded and subjected to up to one lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. DT:2017-01-17T00:00:00+0000 PG:SCS SM:EGAN00001277178 CN:SC @PG ID:SCS PN:RTA VN:1.18.66.3 DS:Controlling software on instrument @PG ID:basecalling PN:RTA PP:SCS VN:1.18.66.3 DS:Basecalling Package @PG ID:bambi PN:bambi PP:basecalling VN:0.9.4 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi i2b --intensity-dir=/nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities --basecalls-dir=/nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BaseCalls --lane=1 --platform-unit=170117_HS33_21698_A_CA42YANXX_1 --read-group-id=21698_1 --study-name="EGAS00001000570: Genomic libraries will be generated from total genomic DNA derived from 4000 samples with Acute Myeloid Leukaemia. Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 64 Samples will be individually barcoded and subjected to up to one lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing. " --sample-alias=EGAN00001277159,EGAN00001277160,EGAN00001277161,EGAN00001277162,EGAN00001277163,EGAN00001277164,EGAN00001277165,EGAN00001277166,EGAN00001277167,EGAN00001277168,EGAN00001277169,EGAN00001277170,EGAN00001277171,EGAN00001277172,EGAN00001277173,EGAN00001277174,EGAN00001277175,EGAN00001277176,EGAN00001277177,EGAN00001277178,EGAN00001277179,EGAN00001277180,EGAN00001277181,EGAN00001277182 --output-file=- --compression-level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:bambi VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamadapterfind level=0 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.9.4 CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi decode --metrics-file /nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/21698_1.bam.tag_decode.metrics --barcode-file /nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/metadata_cache_21698/lane_1.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 PP:bambi.1 VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamcollate2 collate=2 level=0 @PG ID:bwa PN:bwa PP:bamcollate2 VN:0.7.15-r1140 CL:/software/solexa/pkg/bwa/0.7.15/bwa sampe /lustre/scratch110/srpipe/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/6MqhdjTz0F/alnphix_bwa_aln_1_out /tmp/zFBL85qTRo/alnphix_bwa_aln_2_out /tmp/4bb4Xe4pzQ/alnphix_simple_cat1_out /tmp/gm0DNRjAsT/alnphix_simple_cat2_out @PG ID:scramble PN:scramble PP:bwa VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -t 2 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/V_FrtaFH3m/simple_cat_out @PG ID:scramble.1 PN:scramble PP:bam12auxmerge VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -I bam -O cram -x -3 @PG ID:scramble.2 PN:scramble PP:scramble.1 VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -I cram -O bam -0 @PG ID:spf PN:spatial_filter PP:scramble.2 DS:A program to apply a spatial filter VN:v10.27-dirty CL:/software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/no_cal/archive/qc/tileviz/21698_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 /dev/stdin ; /software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -a -f -u -l /nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/no_cal/21698_1.bam.filter.stats -F /tmp/ZqW8p9Y6c9/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.3.1-npg-Sep2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-Dec2016/bin/samtools split -f /nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/no_cal/lane1/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 PP:samtools VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2' VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamadapterclip verbose=0 level=0 @PG ID:bwa' PN:bwa PP:bamadapterclip VN:0.7.15-r1140 CL:/software/solexa/pkg/bwa/0.7.15/bwa mem -t 12 -p -Y -K 100000000 /lustre/scratch110/srpipe/references/Homo_sapiens/CGP_GRCh37.NCBI.allchr_MT/all/bwa0_6/Homo_sapiens.GRCh37.NCBI.allchr_MT.fa /tmp/_IxNJUrdTX/alntgt_bamtofastq_out @PG ID:scramble' PN:scramble PP:bwa' VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam @PG ID:samtools' PN:samtools PP:scramble' VN:1.3.1-npg-Sep2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-Dec2016/bin/samtools reheader /tmp/wsEwxNgqJ4/postalntgt_alterSQ_headerSQfix_out /tmp/4Nruh7JeJY/postalntgt_mbuffer_headerSQfix_out @PG ID:bam12split PN:bam12split PP:samtools' VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12split verbose=0 level=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamsormadup threads=12 SO=queryname level=0 @PG ID:bam12auxmerge' PN:bam12auxmerge PP:bamsormadup VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/Blhr1_alyq/amp_bamadapterclip_pre_auxmerge_out @PG ID:AlignmentFilter PN:AlignmentFilter PP:bam12auxmerge' 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:V1.19 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_21698_1#20.bam, /tmp/GEkQuRFkuY/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/5xDtHbgeDe/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=21698_1#20.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:bamsormadup' PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamsormadup threads=12 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/no_cal/archive/lane1/bsfopt_21698_1#20.tmp PP:AlignmentFilter VN:2.0.65 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/no_cal/archive/lane1/bmdfopt_21698_1#20.tmp M=/nfs/sf47/ILorHSany_sf47/analysis/170117_HS33_21698_A_CA42YANXX/Data/Intensities/BAM_basecalls_20170121-190337/no_cal/archive/lane1/21698_1#20.markdups_metrics.txt PP:bamsormadup' VN:2.0.65 @PG ID:scramble.3 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -t 5 -7 -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 @CO TY:checksum ST:all PA:all HA:crc32prod CO:29722570 BS:338febce NS:24141f21 SQ:5e2fff2 ST:BC,FI,QT,RT,TC:689348b2 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:29722570 BS:338febce NS:24141f21 SQ:5e2fff2 ST:BC,FI,QT,RT,TC:689348b2 @CO TY:checksum ST: PA:all HA:crc32prod CO:0 BS:1 NS:1 SQ:1 ST:BC,FI,QT,RT,TC:1 @CO TY:checksum ST: PA:pass HA:crc32prod CO:0 BS:1 NS:1 SQ:1 ST:BC,FI,QT,RT,TC:1 @CO TY:checksum ST:21698_1#20 PA:all HA:crc32prod CO:29722570 BS:338febce NS:24141f21 SQ:5e2fff2 ST:BC,FI,QT,RT,TC:689348b2 @CO TY:checksum ST:21698_1#20 PA:pass HA:crc32prod CO:29722570 BS:338febce NS:24141f21 SQ:5e2fff2 ST:BC,FI,QT,RT,TC:689348b2 @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