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UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:efc49c871536fa8d79cb0a06fa739722 SP:Human @SQ SN:GL000198.1 LN:90085 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:868e7784040da90d900d2d1b667a1383 SP:Human @SQ SN:GL000208.1 LN:92689 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Human @SQ SN:GL000191.1 LN:106433 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Human @SQ SN:GL000227.1 LN:128374 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:a4aead23f8053f2655e468bcc6ecdceb SP:Human @SQ SN:GL000228.1 LN:129120 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Human @SQ SN:GL000214.1 LN:137718 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:46c2032c37f2ed899eb41c0473319a69 SP:Human @SQ SN:GL000221.1 LN:155397 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:3238fb74ea87ae857f9c7508d315babb SP:Human @SQ SN:GL000209.1 LN:159169 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Human @SQ SN:GL000218.1 LN:161147 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Human @SQ SN:GL000220.1 LN:161802 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fc35de963c57bf7648429e6454f1c9db SP:Human @SQ SN:GL000213.1 LN:164239 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:9d424fdcc98866650b58f004080a992a SP:Human @SQ SN:GL000211.1 LN:166566 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Human @SQ SN:GL000199.1 LN:169874 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:569af3b73522fab4b40995ae4944e78e SP:Human @SQ SN:GL000217.1 LN:172149 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Human @SQ SN:GL000216.1 LN:172294 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:642a232d91c486ac339263820aef7fe0 SP:Human @SQ SN:GL000215.1 LN:172545 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5eb3b418480ae67a997957c909375a73 SP:Human @SQ SN:GL000205.1 LN:174588 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Human @SQ SN:GL000219.1 LN:179198 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Human @SQ SN:GL000224.1 LN:179693 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Human @SQ SN:GL000223.1 LN:180455 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Human @SQ SN:GL000195.1 LN:182896 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5d9ec007868d517e73543b005ba48535 SP:Human @SQ SN:GL000212.1 LN:186858 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:563531689f3dbd691331fd6c5730a88b SP:Human @SQ SN:GL000222.1 LN:186861 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Human @SQ SN:GL000200.1 LN:187035 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Human @SQ SN:GL000193.1 LN:189789 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:26304_5#10 DT:2018-07-12T00:00:00+0000 PU:180712_HF2_26304_A_HW5CYBBXX_5#10 LB:21452327 PG:SCS SM:EGAN00001746197 CN:SC PL:ILLUMINA DS:EGAS00001002858: Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from breast tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will sample from a wide age range of individuals (<20 to >70 years old) to determine whether these processes differ in pre- and post-menopausal women. We will also be comparing the tissue from healthy individuals (samples from breast reduction surgery) to those at elevated risk of breast cancer (mastectomy from BRCA1/2 patients) and those who have breast cancer (adjacent normal, distal normal, and tumour tissue from mastectomy). This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumour development. @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/sciops/pkg/bambi/0.11.1/bin/bambi i2b --intensity-dir=/nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities --basecalls-dir=/nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BaseCalls --lane=5 --platform-unit=180712_HF2_26304_A_HW5CYBBXX_5 --read-group-id=26304_5 --study-name="EGAS00001002858: Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from breast tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will sample from a wide age range of individuals (<20 to >70 years old) to determine whether these processes differ in pre- and post-menopausal women. We will also be comparing the tissue from healthy individuals (samples from breast reduction surgery) to those at elevated risk of breast cancer (mastectomy from BRCA1/2 patients) and those who have breast cancer (adjacent normal, distal normal, and tumour tissue from mastectomy). This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumour development. " --sample-alias=EGAN00001746172,EGAN00001746174,EGAN00001746175,EGAN00001746182,EGAN00001746183,EGAN00001746187,EGAN00001746188,EGAN00001746189,EGAN00001746190,EGAN00001746197,EGAN00001746202,EGAN00001746205,EGAN00001746207,EGAN00001746210,EGAN00001746218,EGAN00001746220,EGAN00001746222,EGAN00001746232,EGAN00001746234,EGAN00001746238,EGAN00001746240,EGAN00001746243,EGAN00001746248,EGAN00001746250,EGAN00001746253,EGAN00001746254,EGAN00001746255,EGAN00001746256,EGAN00001746257,EGAN00001746259,EGAN00001746261,EGAN00001746264 --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/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/26304_5.bam.tag_decode.metrics --barcode-file /nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/metadata_cache_26304/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/23pAIhRLvL/alnphix_bwa_aln_1_out /tmp/s6_7o_i0iF/alnphix_bwa_aln_2_out /tmp/P2eF8A8OP_/alnphix_simple_cat1_out /tmp/XPL0ucNQAU/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/y_89PqFe8Z/simple_cat_out PP:scramble VN:2.0.79 @PG ID:samtools PN:samtools PP:bam12auxmerge VN:1.8-36-gcd71974 CL:/software/sciops/pkg/samtools/1.8+36_gcd71974/bin/samtools split --threads 4 -f /nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/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/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/no_cal/archive/qc/tileviz/26304_5 -F /dev/stdout /dev/stdin ; /software/sciops/pkg/bambi/0.11.1/bin/bambi spatial_filter -a --compression-level 0 -f -l /nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/no_cal/archive/lane5/26304_5#10.spatial_filter.stats -F /nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/no_cal/26304_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 16 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/Ko2M8lA8kw/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+36_gcd71974/bin/samtools reheader /tmp/RxQTBk4KHQ/aln_postaln_alterSQ_headerSQfix_out /tmp/_jiPgBGaHB/aln_postaln_mbuffer_headerSQfix_out PP:scramble' VN:1.8-36-gcd71974 @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/EvflkPrSgk/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/nXemcQhL64/aln_tee3_tee3:to_phix_aln_out,/tmp/IhbCgSViaN/aln_bam12auxmerge_out --output /tmp/2Q7LWy5F77/alignment_filter:phix_bam_out_out,/tmp/ibH55a6mTJ/alignment_filter:target_bam_out_out -m 26304_5#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=16 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/no_cal/archive/lane5/bsfopt_26304_5#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/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/no_cal/archive/lane5/bmdfopt_26304_5#10.tmp M=/nfs/sf30/ILorHSany_sf30/analysis/180712_HF2_26304_A_HW5CYBBXX/Data/Intensities/BAM_basecalls_20180715-150845/no_cal/archive/lane5/26304_5#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 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:18831786 BS:5ed0c625 NS:50b7ee33 SQ:6d02c189 ST:BC,FI,QT,RT,TC:714a3a6d @CO TY:checksum ST:all PA:pass HA:crc32prod CO:18810680 BS:7a1c3607 NS:52b4fbf1 SQ:699ed174 ST:BC,FI,QT,RT,TC:7cd89e7e @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:26304_5#10 PA:all HA:crc32prod CO:18831786 BS:5ed0c625 NS:50b7ee33 SQ:6d02c189 ST:BC,FI,QT,RT,TC:714a3a6d @CO TY:checksum ST:26304_5#10 PA:pass HA:crc32prod CO:18810680 BS:7a1c3607 NS:52b4fbf1 SQ:699ed174 ST:BC,FI,QT,RT,TC:7cd89e7e