@HD VN:1.4 SO:coordinate @RG ID:22003_2#19 PL:ILLUMINA PU:170227_HX1_22003_A_HHWGHALXX_2#19 LB:18653486 DS:EGAS00001002222: Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. DT:2017-02-27T00:00:00+0000 PG:SCS SM:EGAN00001496967 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:0.9.4 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi i2b --intensity-dir=/nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities --basecalls-dir=/nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BaseCalls --lane=2 --platform-unit=170227_HX1_22003_A_HHWGHALXX_2 --read-group-id=22003_2 --study-name="EGAS00001002222: Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.,EGAS00001002167: This is a continuation of the osteosarcoma work we have undertaken.,EGAS00001002252: The aims of the study is to: 1. To map double strand breaks introduced genome-wide and to monitor their repair, leading to mechanistic insights into the repair process and the genetic control of discrete steps. 2. To understand how cell coordinates the activities of multiple DNA repair pathways that respond to DNA DSBs and how the relative importance of these different systems is modulated during cell cycle transition/ and in different cells (i.e. BRCA mutants vs. BRCA normal; cancer vs. normal). 3. To understand the cellular and molecular requirements that govern the genesis of genomic rearrangements.,EGAS00001001382: ***THIS DATA CAN ONLY BE USED FOR NON-COMMERCIAL CANCER RESEARCH*** Sequencing of organoid cell lines derived from oesophageal tumour sections taken from patients diagnosed with primary oesophageal cancer who underwent tumour resection surgery. " --sample-alias=3767STDY6717046,3767STDY6717047,EGAN00001496955,EGAN00001496956,EGAN00001496957,EGAN00001496958,EGAN00001496959,EGAN00001496960,EGAN00001496961,EGAN00001500849,EGAN00001500850,EGAN00001500851,EGAN00001500852,EGAN00001496962,EGAN00001496963,EGAN00001496964,EGAN00001496965,EGAN00001496966,EGAN00001496967,EGAN00001496941,EGAN00001496942,EGAN00001496943,EGAN00001496997,EGAN00001496998,EGAN00001496999,EGAN00001497000,EGAN00001497001,EGAN00001497002,EGAN00001497003,EGAN00001497004,EGAN00001497005,EGAN00001497006,EGAN00001497007,EGAN00001497008,EGAN00001497009,EGAN00001497010,EGAN00001497011,EGAN00001497012,EGAN00001496968,EGAN00001500853,EGAN00001500848,EGAN00001496969 --output-file=- --compression-level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:bambi VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamadapterfind level=0 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.9.4 CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi decode --metrics-file /nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/22003_2.bam.tag_decode.metrics --barcode-file /nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/metadata_cache_22003/lane_2.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 PP:bambi.1 VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/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/J8vt_Wtypn/alnphix_bwa_aln_1_out /tmp/ob1VORx5Xe/alnphix_bwa_aln_2_out /tmp/fz08KJeM0Y/alnphix_simple_cat1_out /tmp/1wvz8krTc6/alnphix_simple_cat2_out @PG ID:scramble PN:scramble PP:bwa VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -t 2 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/Azyq61nPd_/simple_cat_out @PG ID:scramble.1 PN:scramble PP:bam12auxmerge VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -I bam -O cram -x -3 @PG ID:scramble.2 PN:scramble PP:scramble.1 VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/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:v10.27-dirty CL:/software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/no_cal/archive/qc/tileviz/22003_2 --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/10.27/bin/spatial_filter -a -f -u -l /nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/no_cal/22003_2.bam.filter.stats -F /tmp/CMp3kjRsMW/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.3.1-npg-Sep2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-Dec2016/bin/samtools split -f /nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/no_cal/lane2/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 PP:samtools VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2' VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/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/ZZ3qGbtvku/alntgt_bamtofastq_out @PG ID:scramble' PN:scramble PP:bwa' VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/bin/scramble -0 -I sam -O bam @PG ID:samtools' PN:samtools PP:scramble' VN:1.3.1-npg-Sep2016 CL:/software/solexa/pkg/samtools/1.3.1-npg-Dec2016/bin/samtools reheader /tmp/jP95v0ugDw/postalntgt_alterSQ_headerSQfix_out /tmp/AizcRvqi5i/postalntgt_mbuffer_headerSQfix_out @PG ID:bam12split PN:bam12split PP:samtools' VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12split verbose=0 level=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamsormadup threads=16 SO=queryname level=0 @PG ID:bam12auxmerge' PN:bam12auxmerge PP:bamsormadup VN:2.0.65 CL:/software/solexa/pkg/biobambam/2.0.65/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/g1F55gdSQT/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_22003_2#19.bam, /tmp/ZAXiBUMMQk/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/7aK0aJL3h9/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=22003_2#19.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/2.0.65/bin/bamsormadup threads=16 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/no_cal/archive/lane2/bsfopt_22003_2#19.tmp PP:AlignmentFilter VN:2.0.65 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.65/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/no_cal/archive/lane2/bmdfopt_22003_2#19.tmp M=/nfs/sf18/ILorHSany_sf18/analysis/170227_HX1_22003_A_HHWGHALXX/Data/Intensities/BAM_basecalls_20170320-133018/no_cal/archive/lane2/22003_2#19.markdups_metrics.txt PP:bamsormadup' VN:2.0.65 @PG ID:scramble.3 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.8 CL:/software/solexa/pkg/scramble/1.14.8/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:20453290 BS:533f79ea NS:3b3b14e3 SQ:53dfb8f7 ST:BC,FI,QT,RT,TC:476a377 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:20439704 BS:751a0d43 NS:1c4dfaa7 SQ:16aafb96 ST:BC,FI,QT,RT,TC:17e0268e @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:22003_2#19 PA:all HA:crc32prod CO:20453290 BS:533f79ea NS:3b3b14e3 SQ:53dfb8f7 ST:BC,FI,QT,RT,TC:476a377 @CO TY:checksum ST:22003_2#19 PA:pass HA:crc32prod CO:20439704 BS:751a0d43 NS:1c4dfaa7 SQ:16aafb96 ST:BC,FI,QT,RT,TC:17e0268e @SQ SN:1 LN:249250621 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Human @SQ SN:2 LN:243199373 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:a0d9851da00400dec1098a9255ac712e SP:Human @SQ SN:3 LN:198022430 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Human @SQ SN:4 LN:191154276 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:23dccd106897542ad87d2765d28a19a1 SP:Human @SQ SN:5 LN:180915260 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:0740173db9ffd264d728f32784845cd7 SP:Human @SQ SN:6 LN:171115067 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1d3a93a248d92a729ee764823acbbc6b SP:Human @SQ SN:7 LN:159138663 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:618366e953d6aaad97dbe4777c29375e SP:Human @SQ SN:8 LN:146364022 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:96f514a9929e410c6651697bded59aec SP:Human @SQ SN:9 LN:141213431 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:3e273117f15e0a400f01055d9f393768 SP:Human @SQ SN:10 LN:135534747 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:988c28e000e84c26d552359af1ea2e1d SP:Human @SQ SN:11 LN:135006516 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Human @SQ SN:12 LN:133851895 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:51851ac0e1a115847ad36449b0015864 SP:Human @SQ SN:13 LN:115169878 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:283f8d7892baa81b510a015719ca7b0b SP:Human @SQ SN:14 LN:107349540 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:98f3cae32b2a2e9524bc19813927542e SP:Human @SQ SN:15 LN:102531392 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:e5645a794a8238215b2cd77acb95a078 SP:Human @SQ SN:16 LN:90354753 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Human @SQ SN:17 LN:81195210 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Human @SQ SN:18 LN:78077248 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Human @SQ SN:19 LN:59128983 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1aacd71f30db8e561810913e0b72636d SP:Human @SQ SN:20 LN:63025520 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Human @SQ SN:21 LN:48129895 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:2979a6085bfe28e3ad6f552f361ed74d SP:Human @SQ SN:22 LN:51304566 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:a718acaa6135fdca8357d5bfe94211dd SP:Human @SQ SN:X LN:155270560 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Human @SQ SN:Y LN:59373566 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Human @SQ SN:MT LN:16569 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:c68f52674c9fb33aef52dcf399755519 SP:Human @SQ SN:GL000207.1 LN:4262 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Human @SQ SN:GL000226.1 LN:15008 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Human @SQ SN:GL000229.1 LN:19913 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Human @SQ SN:GL000231.1 LN:27386 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Human @SQ SN:GL000210.1 LN:27682 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:851106a74238044126131ce2a8e5847c SP:Human @SQ SN:GL000239.1 LN:33824 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:99795f15702caec4fa1c4e15f8a29c07 SP:Human @SQ SN:GL000235.1 LN:34474 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Human @SQ SN:GL000201.1 LN:36148 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Human @SQ SN:GL000247.1 LN:36422 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UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:1d78abec37c15fe29a275eb08d5af236 SP:Human @SQ SN:GL000196.1 LN:38914 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Human @SQ SN:GL000248.1 LN:39786 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:5a8e43bec9be36c7b49c84d585107776 SP:Human @SQ SN:GL000244.1 LN:39929 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:0996b4475f353ca98bacb756ac479140 SP:Human @SQ SN:GL000238.1 LN:39939 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa AS:NCBI37 M5:131b1efc3270cc838686b54e7c34b17b SP:Human @SQ SN:GL000202.1 LN:40103 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