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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:25949_1#30 DT:2018-05-25T00:00:00+0000 PU:180525_HF2_25949_A_HV5TLBBXX_1#30 LB:15875561 PG:SCS SM:EGAN00001702306 CN:SC PL:ILLUMINA DS:EGAS00001002935: We aim to describe the transcriptomic landscape of infant spindle cell tumours. @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:0.11.1 CL:/software/solexa/pkg/bambi/0.11.1/bin/bambi i2b --intensity-dir=/nfs/sf30/ILorHSany_sf30/analysis/180525_HF2_25949_A_HV5TLBBXX/Data/Intensities --basecalls-dir=/nfs/sf30/ILorHSany_sf30/analysis/180525_HF2_25949_A_HV5TLBBXX/Data/Intensities/BaseCalls --lane=1 --platform-unit=180525_HF2_25949_A_HV5TLBBXX_1 --read-group-id=25949_1 --study-name="EGAS00001002935: We aim to describe the transcriptomic landscape of infant spindle cell tumours." --sample-alias=EGAN00001702277,EGAN00001702278,EGAN00001702279,EGAN00001702280,EGAN00001702281,EGAN00001702282,EGAN00001702283,EGAN00001702284,EGAN00001702285,EGAN00001702286,EGAN00001702287,EGAN00001702288,EGAN00001702289,EGAN00001702290,EGAN00001702291,EGAN00001702292,EGAN00001702293,EGAN00001702294,EGAN00001702295,EGAN00001702296,EGAN00001702297,EGAN00001702298,EGAN00001702299,EGAN00001702300,EGAN00001702301,EGAN00001702302,EGAN00001702303,EGAN00001702304,EGAN00001702305,EGAN00001702306,EGAN00001702307,EGAN00001702308,EGAN00001702309,EGAN00001702310,EGAN00001702311,EGAN00001702312,EGAN00001702313,EGAN00001702314 --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/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:0.11.1 CL:/software/solexa/pkg/bambi/0.11.1/bin/bambi decode --metrics-file /nfs/sf30/ILorHSany_sf30/analysis/180525_HF2_25949_A_HV5TLBBXX/Data/Intensities/BAM_basecalls_20180605-093738/25949_1.bam.tag_decode.metrics --barcode-file /nfs/sf30/ILorHSany_sf30/analysis/180525_HF2_25949_A_HV5TLBBXX/Data/Intensities/BAM_basecalls_20180605-093738/metadata_cache_25949/lane_1.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/ezuLUsgL0w/alnphix_bwa_aln_1_out /tmp/BfU5Mh3WCV/alnphix_bwa_aln_2_out /tmp/uaqhIFFBV1/alnphix_simple_cat1_out /tmp/KFdCojUO_m/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 5 -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/X6elqrETPH/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:0.11.1 CL:/software/solexa/pkg/bambi/0.11.1/bin/bambi spatial_filter -c -t /nfs/sf30/ILorHSany_sf30/analysis/180525_HF2_25949_A_HV5TLBBXX/Data/Intensities/BAM_basecalls_20180605-093738/no_cal/archive/qc/tileviz/25949_1 -F /dev/stdout /dev/stdin ; /software/solexa/pkg/bambi/0.11.1/bin/bambi spatial_filter -a --compression-level 0 -f -F /tmp/yk3aWU7QHw/tee_post_filter_creation:__APPLY_FILTER_OUT___out -l /nfs/sf30/ILorHSany_sf30/analysis/180525_HF2_25949_A_HV5TLBBXX/Data/Intensities/BAM_basecalls_20180605-093738/no_cal/25949_1.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/sf30/ILorHSany_sf30/analysis/180525_HF2_25949_A_HV5TLBBXX/Data/Intensities/BAM_basecalls_20180605-093738/no_cal/lane1/%!.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 24 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/Epzfzn0Mhk/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/akLNZt0Xhb/aln_postaln_alterSQ_headerSQfix_out /tmp/qBs1KxESnU/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/f8zcu3cFxI/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/solexa/pkg/bambi/0.11.1/bin/bambi select --compression-level 0 --input /tmp/u7_2WdlTCd/aln_tee3_tee3:to_phix_aln_out,/tmp/m0T8fhJlg_/aln_bam12auxmerge_out --output 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PA:pass HA:crc32prod CO:13189372 BS:11fff7a7 NS:4196fe5c SQ:1de14692 ST:BC,FI,QT,RT,TC:6c7c3db6