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UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Human @SQ SN:GL000194.1 LN:191469 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Human @SQ SN:GL000225.1 LN:211173 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:63945c3e6962f28ffd469719a747e73c SP:Human @SQ SN:GL000192.1 LN:547496 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Human @SQ SN:NC_007605 LN:171823 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Human @SQ SN:hs37d5 LN:35477943 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1 SP:Human @RG ID:25543_2#15 DT:2018-03-28T00:00:00+0000 PU:180328_HF1_25543_A_HTG7GBBXX_2#15 LB:20685112 PG:SCS SM:sc_autozygELGH7221072 CN:SC PL:ILLUMINA DS:EGAS00001002742: This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ @PG ID:SCS VN:HD 3.4.0.38 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:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi i2b --intensity-dir=/nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities --basecalls-dir=/nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BaseCalls --lane=2 --platform-unit=180328_HF1_25543_A_HTG7GBBXX_2 --read-group-id=25543_2 --study-name="EGAS00001002742: This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/" --sample-alias=sc_autozygELGH7221057,sc_autozygELGH7221058,sc_autozygELGH7221059,sc_autozygELGH7221060,sc_autozygELGH7221061,sc_autozygELGH7221062,sc_autozygELGH7221063,sc_autozygELGH7221064,sc_autozygELGH7221065,sc_autozygELGH7221066,sc_autozygELGH7221067,sc_autozygELGH7221068,sc_autozygELGH7221069,sc_autozygELGH7221071,sc_autozygELGH7221072,sc_autozygELGH7221074,sc_autozygELGH7221075,sc_autozygELGH7221076,sc_autozygELGH7221077,sc_autozygELGH7221078,sc_autozygELGH7221079,sc_autozygELGH7221081,sc_autozygELGH7221082,sc_autozygELGH7221083 --threads=3 --output-file=- --compression-level=0 PN:bambi DS:Convert Illumina BCL to BAM or SAM file @PG ID:bamadapterfind PN:bamadapterfind CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamadapterfind level=0 PP:bambi VN:2.0.79 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi decode --metrics-file /nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/25543_2.bam.tag_decode.metrics --barcode-file /nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/metadata_cache_25543/lane_2.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamcollate2 collate=2 level=0 PP:bambi.1 VN:2.0.79 @PG ID:bwa PN:bwa CL:/software/solexa/pkg/bwa/0.7.16a/bwa sampe /lustre/scratch117/core/sciops_repository/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/3D5jrA6GCB/alnphix_bwa_aln_1_out /tmp/DpNHRKhLnW/alnphix_bwa_aln_2_out /tmp/hZxia5lEle/alnphix_simple_cat1_out /tmp/a09bbJoETY/alnphix_simple_cat2_out PP:bamcollate2 VN:0.7.16a-r1181 @PG ID:scramble PN:scramble CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -t 1 -I sam -O bam PP:bwa VN:1.14.9 @PG ID:bam12auxmerge PN:bam12auxmerge CL:/software/solexa/pkg/biobambam/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/ukFjKHIOq_/simple_cat_out PP:scramble VN:2.0.79 @PG ID:scramble.1 PN:scramble PP:bam12auxmerge VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -I bam -O cram -x -3 @PG ID:scramble.2 PN:scramble PP:scramble.1 VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/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:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi spatial_filter -c -t /nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/no_cal/archive/qc/tileviz/25543_2 -F /dev/stdout /dev/stdin ; /software/solexa/pkg/bambi/0.10.1/bin/bambi spatial_filter -a --compression-level 0 -f -F /tmp/aXcrJYwKZk/tee_post_filter_creation:__APPLY_FILTER_OUT___out -l /nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/no_cal/25543_2.bam.filter.stats /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.6 CL:/software/solexa/pkg/samtools/1.6/bin/samtools split -f /nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/no_cal/lane2/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamcollate2 collate=1 level=0 PP:samtools VN:2.0.79 @PG ID:bamreset PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamreset resetaux=0 level=0 verbose=0 PP:bamcollate2' VN:2.0.79 @PG ID:bamadapterclip PN:bamadapterclip CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamadapterclip verbose=0 level=0 PP:bamreset VN:2.0.79 @PG ID:bwa' PN:bwa CL:/software/solexa/pkg/bwa/0.7.16a/bwa mem -t 8 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/ivCMws4QUC/aln_alntgt_bamtofastq_out PP:bamadapterclip VN:0.7.16a-r1181 @PG ID:scramble' PN:scramble CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -I sam -O bam PP:bwa' VN:1.14.9 @PG ID:samtools' PN:samtools CL:/software/solexa/pkg/samtools/1.6/bin/samtools reheader /tmp/IUOwj2n8Bv/aln_postaln_alterSQ_headerSQfix_out /tmp/KrqBKLej6t/aln_postaln_mbuffer_headerSQfix_out PP:scramble' VN:1.6 @PG ID:bam12split PN:bam12split CL:/software/solexa/pkg/biobambam/2.0.79/bin/bam12split verbose=0 level=0 PP:samtools' VN:2.0.79 @PG ID:bam12auxmerge' PN:bam12auxmerge CL:/software/solexa/pkg/biobambam/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/20P71Jdhfr/aln_amp_bamadapterclip_pre_auxmerge_out PP:bam12split VN:2.0.79 @PG ID:bambi.2 PN:bambi PP:bam12auxmerge' VN:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi select --compression-level 0 --input /tmp/f064nQkaVs/aln_tee3_tee3:to_phix_aln_out,/tmp/gwx_NyShpl/aln_bam12auxmerge_out --output /tmp/fH11AUJsJt/alignment_filter:phix_bam_out_out,/tmp/GPA7OT6tko/alignment_filter:target_bam_out_out -m 25543_2#15.bam_alignment_filter_metrics.json DS:Split alignments into different files @PG ID:bamsormadup PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamsormadup threads=8 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/no_cal/archive/lane2/bsfopt_25543_2#15.tmp PP:bambi.2 VN:2.0.79 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/no_cal/archive/lane2/bmdfopt_25543_2#15.tmp M=/nfs/sf29/ILorHSany_sf29/analysis/180328_HF1_25543_A_HTG7GBBXX/Data/Intensities/BAM_basecalls_20180330-073646/no_cal/archive/lane2/25543_2#15.markdups_metrics.txt PP:bamsormadup VN:2.0.79 @PG ID:scramble.3 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -t 3 -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:21431366 BS:501bf20 NS:7f1ed9ba SQ:5fdde7c1 ST:BC,FI,QT,RT,TC:297d7b2 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:21426368 BS:1dad9527 NS:7c601456 SQ:4e934cad ST:BC,FI,QT,RT,TC:2f7a00d4 @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:25543_2#15 PA:all HA:crc32prod CO:21431366 BS:501bf20 NS:7f1ed9ba SQ:5fdde7c1 ST:BC,FI,QT,RT,TC:297d7b2 @CO TY:checksum ST:25543_2#15 PA:pass HA:crc32prod CO:21426368 BS:1dad9527 NS:7c601456 SQ:4e934cad ST:BC,FI,QT,RT,TC:2f7a00d4