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UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:4e0d459b9bd15bff8645de84334e3d25 AH:* SP:Human @SQ SN:HLA-DRB1*16:02:01 LN:11005 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_full_analysis_set_plus_decoy_hla/all/fasta/Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa AS:GRCh38 M5:4a972df76bd3ee2857b87bd5be5ea00a AH:* SP:Human @RG ID:22373_1#12 PL:ILLUMINA PU:170427_HF1_22373_B_HGYTCBBXX_1#12 LB:18828267 DS:EGAS00001002188: This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2017-04-27T01:00:00+0100 PG:SCS SM:EGAN00001531621 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/sf32/ILorHSany_sf32/analysis/170427_HF1_22373_B_HGYTCBBXX/Data/Intensities --basecalls-dir=/nfs/sf32/ILorHSany_sf32/analysis/170427_HF1_22373_B_HGYTCBBXX/Data/Intensities/BaseCalls --lane=1 --platform-unit=170427_HF1_22373_B_HGYTCBBXX_1 --read-group-id=22373_1 --study-name="EGAS00001002188: This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/" --sample-alias=EGAN00001531610,EGAN00001531611,EGAN00001531612,EGAN00001531613,EGAN00001531614,EGAN00001531615,EGAN00001531616,EGAN00001531617,EGAN00001531618,EGAN00001531619,EGAN00001531620,EGAN00001531621,EGAN00001531622,EGAN00001531623,EGAN00001531624,EGAN00001531625,EGAN00001531626,EGAN00001531627,EGAN00001531628,EGAN00001531629,EGAN00001531630,EGAN00001531631,EGAN00001531632,EGAN00001531633 --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:0.9.4 CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi decode --metrics-file /nfs/sf32/ILorHSany_sf32/analysis/170427_HF1_22373_B_HGYTCBBXX/Data/Intensities/BAM_basecalls_20170515-142752/22373_1.bam.tag_decode.metrics --barcode-file /nfs/sf32/ILorHSany_sf32/analysis/170427_HF1_22373_B_HGYTCBBXX/Data/Intensities/BAM_basecalls_20170515-142752/metadata_cache_22373/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/fx7w0nbCyp/alnphix_bwa_aln_1_out /tmp/_ttjrX7LKM/alnphix_bwa_aln_2_out /tmp/mWaHlRzn5f/alnphix_simple_cat1_out /tmp/5WO2aBoXjC/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/Uy3ws3ShPH/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:v10.27-dirty CL:/software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf32/ILorHSany_sf32/analysis/170427_HF1_22373_B_HGYTCBBXX/Data/Intensities/BAM_basecalls_20170515-142752/no_cal/archive/qc/tileviz/22373_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 /dev/stdin ; 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