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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:23210_1#12 PL:ILLUMINA PU:170726_HF1_23210_A_HKLG5BBXX_1#12 LB:19069976 DS:EGAS00001002221: Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. DT:2017-07-26T01:00:00+0100 PG:SCS SM:EGAN00001514274 CN:SC @PG ID:SCS PN:HiSeq Control Software VN:HD 3.4.0.38 DS:Controlling software on instrument @PG ID:basecalling PN:Unknown PP:SCS VN:Unknown DS:Basecalling Package @PG ID:bambi PN:bambi PP:basecalling VN:0.9.11 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.11/bin/bambi i2b --intensity-dir=/nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities --basecalls-dir=/nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BaseCalls --lane=1 --platform-unit=170726_HF1_23210_A_HKLG5BBXX_1 --read-group-id=23210_1 --study-name="EGAS00001002221: Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients." --sample-alias=EGAN00001514263,EGAN00001514264,EGAN00001514265,EGAN00001514266,EGAN00001514267,EGAN00001514268,EGAN00001514269,EGAN00001514270,EGAN00001514271,EGAN00001514272,EGAN00001514273,EGAN00001514274,EGAN00001514275 --output-file=- --compression-level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:bambi VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamadapterfind level=0 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.9.11 CL:/software/solexa/pkg/bambi/0.9.11/bin/bambi decode --metrics-file /nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/23210_1.bam.tag_decode.metrics --barcode-file /nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/metadata_cache_23210/lane_1.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 PP:bambi.1 VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/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/scratch117/core/sciops_repository/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/3KPtIhnQ7o/alnphix_bwa_aln_1_out /tmp/gqkCKAzACr/alnphix_bwa_aln_2_out /tmp/Qz1TgjSpaw/alnphix_simple_cat1_out /tmp/MBIjo8KwVB/alnphix_simple_cat2_out @PG ID:scramble PN:scramble PP:bwa VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -t 1 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/gdmn1PWtL_/simple_cat_out @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:v10.28-dirty CL:/software/solexa/pkg/pb_calibration/10.28/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/no_cal/archive/qc/tileviz/23210_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/10.28/bin/spatial_filter -a -f -u -l /nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/no_cal/23210_1.bam.filter.stats -F /tmp/2Hn2GEZd8H/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.5 CL:/software/solexa/pkg/samtools/1.5/bin/samtools split -f /nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/no_cal/lane1/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 PP:samtools VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2' VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/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 16 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/m4dEuk_YS3/alntgt_bamtofastq_out @PG ID:scramble' PN:scramble PP:bwa' VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -I sam -O bam @PG ID:samtools' PN:samtools PP:scramble' VN:1.5 CL:/software/solexa/pkg/samtools/1.5/bin/samtools reheader /tmp/PJjfUzTpph/postalntgt_alterSQ_headerSQfix_out /tmp/0IsQG6TlhL/postalntgt_mbuffer_headerSQfix_out @PG ID:bam12split PN:bam12split PP:samtools' VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bam12split verbose=0 level=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamsormadup threads=16 SO=queryname level=0 @PG ID:bam12auxmerge' PN:bam12auxmerge PP:bamsormadup VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/VVx7v77ckL/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_23210_1#12.bam, /tmp/BxVwfqYq_Q/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/us84Q5onPy/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=23210_1#12.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/2.0.72/bin/bamsormadup threads=16 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/no_cal/archive/lane1/bsfopt_23210_1#12.tmp PP:AlignmentFilter VN:2.0.72 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/no_cal/archive/lane1/bmdfopt_23210_1#12.tmp M=/nfs/sf29/ILorHSany_sf29/analysis/170726_HF1_23210_A_HKLG5BBXX/Data/Intensities/BAM_basecalls_20170728-064842/no_cal/archive/lane1/23210_1#12.markdups_metrics.txt PP:bamsormadup' VN:2.0.72 @PG ID:scramble.3 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -t 7 -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:47051480 BS:4e8837f7 NS:48f0802f SQ:49d31e59 ST:BC,FI,QT,RT,TC:2e01f670 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:47043470 BS:2b04e2b3 NS:53ffa4b7 SQ:73b77ae1 ST:BC,FI,QT,RT,TC:6a683ae9 @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:23210_1#12 PA:all HA:crc32prod CO:47051480 BS:4e8837f7 NS:48f0802f SQ:49d31e59 ST:BC,FI,QT,RT,TC:2e01f670 @CO TY:checksum ST:23210_1#12 PA:pass HA:crc32prod CO:47043470 BS:2b04e2b3 NS:53ffa4b7 SQ:73b77ae1 ST:BC,FI,QT,RT,TC:6a683ae9