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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:27645_5#2 DT:2018-11-29T00:00:00+0000 PU:181129_HX5_27645_A_HTNKVCCXY_5#2 LB:22628806 PG:SCS SM:EGAN00001840552 CN:SC PL:ILLUMINA DS:EGAS00001003181: The study will measure blood population dynamics in abnormal human haematopoiesis in patients with clonal blood stem cell disorders. @PG ID:SCS VN:HD 3.5.0.7 PN:HiSeq Control Software DS:Controlling software on instrument @PG ID:basecalling PP:SCS VN:Unknown PN:Unknown 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/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities --basecalls-dir=/nfs/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities/BaseCalls --lane=5 --platform-unit=181129_HX5_27645_A_HTNKVCCXY_5 --read-group-id=27645_5 --study-name="EGAS00001003181: The study will measure blood population dynamics in abnormal human haematopoiesis in patients with clonal blood stem cell disorders." --sample-alias=EGAN00001840485,EGAN00001840552,EGAN00001840463,EGAN00001840497,EGAN00001840486,EGAN00001840469 --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/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities/BAM_basecalls_20181202-134930/27645_5.bam.tag_decode.metrics --barcode-file /nfs/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities/BAM_basecalls_20181202-134930/metadata_cache_27645/lane_5.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/qIOaH_f6yG/alnphix_bwa_aln_1_out /tmp/_maLNQ3gWh/alnphix_bwa_aln_2_out /tmp/CgduzLn3eH/alnphix_simple_cat1_out /tmp/f9GLbwXnVx/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 3 -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/4t2W6GooBi/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/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities/BAM_basecalls_20181202-134930/no_cal/lane5/%!.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/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities/BAM_basecalls_20181202-134930/no_cal/archive/qc/tileviz/27645_5 -F /dev/stdout /dev/stdin ; /software/sciops/pkg/bambi/0.11.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /nfs/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities/BAM_basecalls_20181202-134930/no_cal/archive/lane5/27645_5#2.spatial_filter.stats -F /nfs/sf22/ILorHSany_sf22/analysis/181129_HX5_27645_A_HTNKVCCXY/Data/Intensities/BAM_basecalls_20181202-134930/no_cal/27645_5.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/iFvfCQlxDq/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/GctWfMW7yN/aln_postaln_alterSQ_headerSQfix_out /tmp/eXa2YYRSAg/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/t8o3LZTasp/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/hhzM0tHk66/aln_tee3_tee3:to_phix_aln_out,/tmp/nL7zOAGBYG/aln_bam12auxmerge_out --output /tmp/WGcy_9QYQC/alignment_filter:phix_bam_out_out,/tmp/oSpwcRLwhv/alignment_filter:target_bam_out_out -m 27645_5#2.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 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