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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:27626_3#10 DT:2018-11-29T00:00:00+0000 PU:181129_HX10_27626_B_HVCYGCCXY_3#10 LB:23761380 PG:SCS SM:EGAN00001899040 CN:SC PL:ILLUMINA DS:EGAS00001003162: 12 tissues from the warm autopsy are selected for this project. Using 10X Chromium technology we will generate ~1000 single cell/nulei genomic libraries per tissue. Each tissue will be whole genome sequenced (~2 lanes per 1000 cells) on hiseq X10. per single cell we will generate CNV profile and we investigate the level of genomic heterogenity with in tissue and across different tissues. @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/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities --basecalls-dir=/nfs/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BaseCalls --lane=3 --platform-unit=181129_HX10_27626_B_HVCYGCCXY_3 --read-group-id=27626_3 --study-name="EGAS00001003162: 12 tissues from the warm autopsy are selected for this project. Using 10X Chromium technology we will generate ~1000 single cell/nulei genomic libraries per tissue. Each tissue will be whole genome sequenced (~2 lanes per 1000 cells) on hiseq X10. per single cell we will generate CNV profile and we investigate the level of genomic heterogenity with in tissue and across different tissues. " --sample-alias=EGAN00001899038,EGAN00001899038,EGAN00001899038,EGAN00001899038,EGAN00001899039,EGAN00001899039,EGAN00001899039,EGAN00001899039,EGAN00001899040,EGAN00001899040,EGAN00001899040,EGAN00001899040,EGAN00001899041,EGAN00001899041,EGAN00001899041,EGAN00001899041,EGAN00001899042,EGAN00001899042,EGAN00001899042,EGAN00001899042 --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/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/27626_3.bam.tag_decode.metrics --barcode-file /nfs/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/metadata_cache_27626/lane_3.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/vy4DZP7POb/alnphix_bwa_aln_1_out /tmp/mJMCtRRdww/alnphix_bwa_aln_2_out /tmp/aXetTdT30x/alnphix_simple_cat1_out /tmp/yQocLtWzX6/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/YIal6KpuQa/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/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/no_cal/lane3/%!.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/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/no_cal/archive/qc/tileviz/27626_3 -F /dev/stdout /dev/stdin ; /software/sciops/pkg/bambi/0.11.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /nfs/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/no_cal/archive/lane3/27626_3#10.spatial_filter.stats -F /nfs/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/no_cal/27626_3.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/MMPOPg7VSO/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/wOEQqH9EgZ/aln_postaln_alterSQ_headerSQfix_out /tmp/yUAWqz4zHS/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/dXSHSdxfN1/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/QXzLOLvisM/aln_tee3_tee3:to_phix_aln_out,/tmp/Nm9ypSb9xJ/aln_bam12auxmerge_out --output /tmp/ZrefEXV_9x/alignment_filter:phix_bam_out_out,/tmp/BfJUVt00Hh/alignment_filter:target_bam_out_out -m 27626_3#10.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/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/no_cal/archive/lane3/bsfopt_27626_3#10.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/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/no_cal/archive/lane3/bmdfopt_27626_3#10.tmp M=/nfs/sf42/ILorHSany_sf42/analysis/181129_HX10_27626_B_HVCYGCCXY/Data/Intensities/BAM_basecalls_20181202-064420/no_cal/archive/lane3/27626_3#10.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:225726 BS:34a835 NS:6e845613 SQ:36e130cf ST:BC,FI,QT,RT,TC:6f08a20b @CO TY:checksum ST:all PA:pass HA:crc32prod CO:224834 BS:2ab8a73e NS:7dcff060 SQ:4df9ce08 ST:BC,FI,QT,RT,TC:3c610fca @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:27626_3#10 PA:all HA:crc32prod CO:225726 BS:34a835 NS:6e845613 SQ:36e130cf ST:BC,FI,QT,RT,TC:6f08a20b @CO TY:checksum ST:27626_3#10 PA:pass HA:crc32prod CO:224834 BS:2ab8a73e NS:7dcff060 SQ:4df9ce08 ST:BC,FI,QT,RT,TC:3c610fca