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UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1 SP:Human @RG ID:27010_4#8 DT:2018-09-25T00:00:00+0000 PU:180925_HS34_27010_A_CCV7FANXX_4#8 LB:22608404 PG:SCS SM:5330STDY7580407 CN:SC PL:ILLUMINA DS:EGAS00001003154: DNA and RNA isolated from FFPE blocks of patients who received immune checkpoint inhibition (ICI) are sequenced with the aim to identify therapeutically tractable vulnerabilities in tumors to prevent ICI resistance. @PG ID:SCS VN:1.18.66.3 PN:RTA DS:Controlling software on instrument @PG ID:basecalling PP:SCS VN:1.18.66.3 PN:RTA DS:Basecalling Package @PG ID:bambi PP:basecalling VN:0.11.1 CL:/software/sciops/pkg/bambi/0.11.1/bin/bambi i2b --intensity-dir=/nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities --basecalls-dir=/nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BaseCalls --lane=4 --platform-unit=180925_HS34_27010_A_CCV7FANXX_4 --read-group-id=27010_4 --study-name="EGAS00001003154: DNA and RNA isolated from FFPE blocks of patients who received immune checkpoint inhibition (ICI) are sequenced with the aim to identify therapeutically tractable vulnerabilities in tumors to prevent ICI resistance." --sample-alias=5330STDY7580400,5330STDY7580401,5330STDY7580402,5330STDY7580403,5330STDY7580404,5330STDY7580405,5330STDY7580406,5330STDY7580407,5330STDY7580408,5330STDY7580409,5330STDY7580410,5330STDY7580411,5330STDY7580412,5330STDY7580413,5330STDY7580414,5330STDY7580415,5330STDY7580416,5330STDY7580417,5330STDY7580418,5330STDY7580419,5330STDY7580420,5330STDY7580421,5330STDY7580422,5330STDY7580423 --threads=8 --output-file=- --compression-level=0 PN:bambi DS:Convert Illumina BCL to BAM or SAM file @PG ID:bamadapterfind PN:bamadapterfind CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bamadapterfind level=0 PP:bambi VN:2.0.79 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.11.1 CL:/software/sciops/pkg/bambi/0.11.1/bin/bambi decode --metrics-file /nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/27010_4.bam.tag_decode.metrics --barcode-file /nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/metadata_cache_27010/lane_4.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bamcollate2 collate=2 level=0 PP:bambi.1 VN:2.0.79 @PG ID:bwa PN:bwa CL:/software/sciops/pkg/bwa-aligner/0.7.17/bin/bwa sampe /lustre/scratch117/core/sciops_repository/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/0EBHwaV1vN/alnphix_bwa_aln_1_out /tmp/su8FXIffFA/alnphix_bwa_aln_2_out /tmp/pAv2iKyoJx/alnphix_simple_cat1_out /tmp/asKgQi9eif/alnphix_simple_cat2_out PP:bamcollate2 VN:0.7.17-r1188 @PG ID:scramble PN:scramble CL:/software/sciops/pkg/staden_io_bin/1.14.9/bin/scramble -0 -t 5 -I sam -O bam PP:bwa VN:1.14.9 @PG ID:bam12auxmerge PN:bam12auxmerge CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/f0YneQ50rl/simple_cat_out PP:scramble VN:2.0.79 @PG ID:samtools PN:samtools PP:bam12auxmerge VN:1.8-59-g4da22a9 CL:/software/sciops/pkg/samtools/1.8+59_g4da22a9/bin/samtools split --threads 4 -f /nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/no_cal/lane4/%!.bam - @PG ID:spf PN:spatial_filter PP:samtools DS:A program to apply a spatial filter VN:0.11.1 CL:/software/sciops/pkg/bambi/0.11.1/bin/bambi spatial_filter -c -t /nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/no_cal/archive/qc/tileviz/27010_4 -F /dev/stdout /dev/stdin ; /software/sciops/pkg/bambi/0.11.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/no_cal/archive/lane4/27010_4#8.spatial_filter.stats -F /nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/no_cal/27010_4.spatial_filter /dev/stdin @PG ID:bamcollate2' PN:bamcollate2 CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bamcollate2 collate=1 level=0 PP:spf VN:2.0.79 @PG ID:bamreset PN:bamreset CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bamreset resetaux=0 level=0 verbose=0 PP:bamcollate2' VN:2.0.79 @PG ID:bamadapterclip PN:bamadapterclip CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bamadapterclip verbose=0 level=0 PP:bamreset VN:2.0.79 @PG ID:bwa' PN:bwa CL:/software/sciops/pkg/bwa-aligner/0.7.17/bin/bwa mem -t 24 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/Yp8Nrkmzz_/aln_alntgt_bamtofastq_out PP:bamadapterclip VN:0.7.17-r1188 @PG ID:scramble' PN:scramble CL:/software/sciops/pkg/staden_io_bin/1.14.9/bin/scramble -0 -I sam -O bam PP:bwa' VN:1.14.9 @PG ID:samtools' PN:samtools CL:/software/sciops/pkg/samtools/1.8+59_g4da22a9/bin/samtools reheader /tmp/VDJ0JV25Xf/aln_postaln_alterSQ_headerSQfix_out /tmp/jjowGimBbA/aln_postaln_mbuffer_headerSQfix_out PP:scramble' VN:1.8-59-g4da22a9 @PG ID:bam12split PN:bam12split CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bam12split verbose=0 level=0 PP:samtools' VN:2.0.79 @PG ID:bam12auxmerge' PN:bam12auxmerge CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/9ucE9AcAGd/aln_amp_bamadapterclip_pre_auxmerge_out PP:bam12split VN:2.0.79 @PG ID:bambi.2 PN:bambi PP:bam12auxmerge' VN:0.11.1 CL:/software/sciops/pkg/bambi/0.11.1/bin/bambi select --compression-level 0 --input /tmp/a9TqPRZDGN/aln_tee3_tee3:to_phix_aln_out,/tmp/2xJID3sN5i/aln_bam12auxmerge_out --output /tmp/uf9tLg00Wa/alignment_filter:phix_bam_out_out,/tmp/5xS2lspZlu/alignment_filter:target_bam_out_out -m 27010_4#8.bam_alignment_filter_metrics.json DS:Split alignments into different files @PG ID:bamsormadup PN:bamsormadup CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bamsormadup threads=24 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/no_cal/archive/lane4/bsfopt_27010_4#8.tmp PP:bambi.2 VN:2.0.79 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/sciops/pkg/biobambam2/2.0.79/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/no_cal/archive/lane4/bmdfopt_27010_4#8.tmp M=/nfs/sf50/ILorHSany_sf50/analysis/180925_HS34_27010_A_CCV7FANXX/Data/Intensities/BAM_basecalls_20180929-194532/no_cal/archive/lane4/27010_4#8.markdups_metrics.txt PP:bamsormadup VN:2.0.79 @PG ID:scramble.1 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.9 CL:/software/sciops/pkg/staden_io_bin/1.14.9/bin/scramble -t 11 -7 -I bam -O cram -r /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @CO TY:checksum ST:all PA:all HA:crc32prod CO:23788032 BS:31eebd NS:6e42449e SQ:7066bd54 ST:BC,FI,QT,RT,TC:7e40b4c3 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:23784378 BS:865ce9f NS:569602f4 SQ:64a17979 ST:BC,FI,QT,RT,TC:14800a09 @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:27010_4#8 PA:all HA:crc32prod CO:23788032 BS:31eebd NS:6e42449e SQ:7066bd54 ST:BC,FI,QT,RT,TC:7e40b4c3 @CO TY:checksum ST:27010_4#8 PA:pass HA:crc32prod CO:23784378 BS:865ce9f NS:569602f4 SQ:64a17979 ST:BC,FI,QT,RT,TC:14800a09