@HD VN:1.4 SO:coordinate @RG ID:1#53 PL:ILLUMINA PU:150613_HX2_16545_A_H3KFCCCXX_5#53 LB:14041982 DS:ERP010096: Sequencing of 35 individuals from Tibet to study the demographic history of the region DT:2015-06-13T00:00:00+0100 SM:ERS700555 PG:BamIndexDecoder CN:SC @PG ID:SCS PN:HiSeq X Control Software DS:Controlling software on instrument VN:3.1.26 @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:2.3.9 @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.17 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities BASECALLS_DIR=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BaseCalls LANE=5 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001279035,EGAN00001279043,EGAN00001279051,ERS700538,ERS700533,ERS700544,ERS700555,3613STDY6090726,3613STDY6090774,3613STDY6090797,3613STDY6090808,MSM0.3_s2 STUDY_NAME=EGAS00001001247: This project aims to sequence to high coverage the genomes of 25 individuals from Papua New Guinea, to address population genetic questions relating to the spread of humans outside of Africa and the peopling of Sahul (the continent of Greater Australia). It has still not been established whether all humans outside of Africa descend from a single out-of-Africa migration event, or if Papuans, Australian Aboriginals and related populations in Southeast Asia derive ancestry from a separate, perhaps earlier, migration event. There have been very few genetic studies on these populations and more data is needed to answer these questions. A single set of Papuan samples is publicly available and has been used in hundreds of human population genetic studies, but it is not known to what extent that set is representative of Papuans more generally. Additionally, little is known about the present-day genetic structure of Papuans and Australian Aboriginals. It is not known if there has been gene flow between Australia and Papua New Guinea since the initial settlement of the region around 50,000 years ago, and if so what the effects of such gene flow have been. Likewise, it is not known if the mountainous terrain and very high linguistic diversity of Papua New Guinea is reflected in strong population structure and genetic differentiation between groups. To address these questions, the study design of this project is to sequence small numbers of genomes from several geographically distinct Papuan groups, focusing on the highland regions that are thought to have been more isolated, to enable comparisons between populations within Papua New Guinea and with Australian Aboriginal populations. Data from this project will feed directly into on-going projects on the genetic history of Australia and will also serve as a first look at the population genomics of the Papuan highlands.,Genomel Melanoma Families: Around 10% of patients who present in melanoma clinics have a first degree relative with a previous diagnosis of melanoma. While around 3% have three or more relatives who have been diagnosed with the disease. In this project we will whole genome sequence patients from familial melanoma pedigrees to identify mutations in genes that drive melanomagenesis. The identification of these genes will facilitate the management of familial melanoma patients and their families. ,TBA: Analysis of mutational signatures caused by exposure to known mutagens in human induced pluripotent stem (iPS) cells. A reference human iPS cell-line will be exposed to 100 chemicals known or proposed to be mutagenic. Following exposure to mutagen, cells will undergo a period of recovery before sub clones are generated and sequenced. The progenitor parental IPS cell-line will be used to generate reference sequence data, in order to determine the mutational signatures acquired as a result of exposure to different mutagens.,ERP010096: Sequencing of 35 individuals from Tibet to study the demographic history of the region PLATFORM_UNIT=150613_HX2_16545_A_H3KFCCCXX_5 COMPRESSION_LEVEL=0 GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 LIBRARY_NAME=unknown SEQUENCING_CENTER=SC PLATFORM=ILLUMINA BARCODE_SEQUENCE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT ADD_CLUSTER_INDEX_TAG=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:bamadapterfind PN:bamadapterfind PP:Illumina2bam VN:2.0.8 CL:bamadapterfind level=0 @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.17 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/metadata_cache_16545/lane_5.taglist METRICS_FILE=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/16545_5.bam.tag_decode.metrics VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=false BARCODE_TAG_NAME=BC BARCODE_QUALITY_TAG_NAME=QT MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 CONVERT_LOW_QUALITY_TO_NO_CALL=false MAX_LOW_QUALITY_TO_CONVERT=15 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:spf PN:spatial_filter PP:BamIndexDecoder DS:A program to apply a spatial filter VN:v10.21 CL:/software/solexa/pkg/pb_calibration/v10.21/bin/spatial_filter -c -F pb_align_16545_5.bam.filter -t /nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/no_cal/archive/qc/tileviz/16545_5 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 pb_align_16545_5.bam ; /software/solexa/pkg/pb_calibration/v10.21/bin/spatial_filter -a -f -u -F pb_align_16545_5.bam.filter - @PG ID:bwa PN:bwa PP:spf VN:0.5.10-tpx @PG ID:BamMerger PN:BamMerger PP:bwa DS:A command-line tool to merge BAM/SAM alignment info in the first input file with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM VN:V1.17 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=pb_align_16545_5.bam INPUT=/dev/stdin OUTPUT=16545_5.bam KEEP_EXTRA_UNMAPPED_READS=true REPLACE_ALIGNED_BASE_QUALITY=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true ALIGNMENT_PROGRAM_ID=bwa KEEP_ALL_PG=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs VN:V1.17 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/no_cal/16545_5.bam OUTPUT_PREFIX=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/no_cal/lane5/16545_5 OUTPUT_COMMON_RG_HEAD_TO_TRIM=1 VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:bamcollate2 PN:bamcollate2 PP:SplitBamByReadGroup VN:2.0.8 CL:/software/hpag/biobambam2/2.0.8/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2 VN:2.0.8 CL:/software/hpag/biobambam2/2.0.8/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.8 CL:/software/hpag/biobambam2/2.0.8/bin/bamadapterclip verbose=0 level=0 @PG ID:bwa' PN:bwa PP:bamadapterclip VN:0.7.12-r1039 CL:/software/solexa/pkg/bwa/bwa-0.7.12/bwa mem -t 16 -p -T 0 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa /tmp/dOoLSOdymG/alntgt_bamtofastq_out @PG ID:scramble PN:scramble PP:bwa' VN:1.13.10 CL:/software/solexa/pkg/scramble/io_lib-1.13.10/bin/scramble -I sam -O bam @PG ID:bam12split PN:bam12split PP:scramble VN:2.0.8 CL:/software/hpag/biobambam2/2.0.8/bin/bam12split verbose=0 level=0 @PG ID:bamsort PN:bamsort PP:bam12split VN:2.0.8 CL:/software/hpag/biobambam2/2.0.8/bin/bamsort SO=queryname level=0 @PG ID:AlignmentFilter PN:AlignmentFilter PP:bamsort 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:V1.17 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[./initial_phix_aln_16545_5#53.bam, /tmp/kIqHNVjSaD/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/aucnCtLB_f/alignment_filter:__PHIX_OUTBAM___out, /dev/stdout] METRICS_FILE=16545_5#53.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:bamsort' PN:bamsort CL:/software/hpag/biobambam2/2.0.8/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/no_cal/archive/lane5/bsfopt_16545_5#53.tmp PP:AlignmentFilter VN:2.0.8 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/hpag/biobambam2/2.0.8/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/no_cal/archive/lane5/bmdfopt_16545_5#53.tmp M=/nfs/sf19/ILorHSany_sf19/analysis/150613_HX2_16545_A_H3KFCCCXX/Data/Intensities/BAM_basecalls_20150625-151821/no_cal/archive/lane5/16545_5#53.markdups_metrics.txt PP:bamsort' VN:2.0.8 @PG ID:scramble.1 PN:scramble PP:bamstreamingmarkduplicates VN:1.13.10 CL:/software/solexa/pkg/scramble/io_lib-1.13.10/bin/scramble -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa @PG ID:bamcollate2' PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.16/bin/bamcollate2 inputformat=cram collate=1 level=0 PP:scramble.1 VN:2.0.16 @PG ID:bamreset' PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.16/bin/bamreset resetaux=0 auxfilter=RG,PG,BC,RT,QT,tr,tq,br,qr level=0 verbose=0 PP:bamcollate2' VN:2.0.16 @PG ID:bamadapterfind' PN:bamadapterfind CL:/software/solexa/pkg/biobambam/2.0.16/bin/bamadapterfind clip=1 verbose=0 level=0 PP:bamreset' VN:2.0.16 @PG ID:bwa'' PN:bwa CL:/software/solexa/pkg/bwa/bwa-0.7.12/bwa mem -t 8 -p -T 0 /lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/bwa0_6/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa /tmp/Ee3qQBp6G8/alntgt_bamtofastq_out PP:bamadapterfind' VN:0.7.12-r1039 @PG ID:scramble' PN:scramble CL:/software/solexa/pkg/scramble/1.14.0/bin/scramble -I sam -O bam PP:bwa'' VN:1.14.0 @PG ID:bam12split' PN:bam12split CL:/software/solexa/pkg/biobambam/2.0.16/bin/bam12split verbose=0 level=0 PP:scramble' VN:2.0.16 @PG ID:bamsort'' PN:bamsort CL:/software/solexa/pkg/biobambam/2.0.16/bin/bamsort SO=queryname level=0 PP:bam12split' VN:2.0.16 @PG ID:bamsort''' PN:bamsort CL:/software/solexa/pkg/biobambam/2.0.16/bin/bamsort SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/lustre/scratch110/ensembl/jillian/rt487590_IHTP_MWGS_T19_Tibet_remapping/output/bwa_mem/16545/16545_5#53/bsfopt_16545_5#53.tmp PP:bamsort'' VN:2.0.16 @PG ID:bamstreamingmarkduplicates' PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.16/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/lustre/scratch110/ensembl/jillian/rt487590_IHTP_MWGS_T19_Tibet_remapping/output/bwa_mem/16545/16545_5#53/bmdfopt_16545_5#53.tmp M=/lustre/scratch110/ensembl/jillian/rt487590_IHTP_MWGS_T19_Tibet_remapping/output/bwa_mem/16545/16545_5#53/16545_5#53.markdups_metrics.txt PP:bamsort''' VN:2.0.16 @PG ID:scramble.2 PN:scramble PP:bamstreamingmarkduplicates' VN:1.14.0 CL:/software/solexa/pkg/scramble/1.14.0/bin/scramble -I bam -O cram -r /lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa @SQ SN:chr1 LN:248956422 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:6aef897c3d6ff0c78aff06ac189178dd SP:Human @SQ SN:chr2 LN:242193529 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:f98db672eb0993dcfdabafe2a882905c SP:Human @SQ SN:chr3 LN:198295559 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:76635a41ea913a405ded820447d067b0 SP:Human @SQ SN:chr4 LN:190214555 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:3210fecf1eb92d5489da4346b3fddc6e SP:Human @SQ SN:chr5 LN:181538259 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:a811b3dc9fe66af729dc0dddf7fa4f13 SP:Human @SQ SN:chr6 LN:170805979 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:5691468a67c7e7a7b5f2a3a683792c29 SP:Human @SQ SN:chr7 LN:159345973 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:cc044cc2256a1141212660fb07b6171e SP:Human @SQ SN:chr8 LN:145138636 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:c67955b5f7815a9a1edfaa15893d3616 SP:Human @SQ SN:chr9 LN:138394717 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:6c198acf68b5af7b9d676dfdd531b5de SP:Human @SQ SN:chr10 LN:133797422 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:c0eeee7acfdaf31b770a509bdaa6e51a SP:Human @SQ SN:chr11 LN:135086622 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:1511375dc2dd1b633af8cf439ae90cec SP:Human @SQ SN:chr12 LN:133275309 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:96e414eace405d8c27a6d35ba19df56f SP:Human @SQ SN:chr13 LN:114364328 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:a5437debe2ef9c9ef8f3ea2874ae1d82 SP:Human @SQ SN:chr14 LN:107043718 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:e0f0eecc3bcab6178c62b6211565c807 SP:Human @SQ SN:chr15 LN:101991189 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:f036bd11158407596ca6bf3581454706 SP:Human @SQ SN:chr16 LN:90338345 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:db2d37c8b7d019caaf2dd64ba3a6f33a SP:Human @SQ SN:chr17 LN:83257441 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:f9a0fb01553adb183568e3eb9d8626db SP:Human @SQ SN:chr18 LN:80373285 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:11eeaa801f6b0e2e36a1138616b8ee9a SP:Human @SQ SN:chr19 LN:58617616 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:85f9f4fc152c58cb7913c06d6b98573a SP:Human @SQ SN:chr20 LN:64444167 UR:/lustre/scratch109/srpipe/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:b18e6c531b0bd70e949a7fc20859cb01 SP:Human @SQ SN:chr21 LN:46709983 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