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SP:Human @SQ SN:chrUn_KI270396v1 LN:1880 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:9069bed3c2efe7cc87227d619ad5816f SP:Human @SQ SN:chrUn_KI270388v1 LN:1216 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:76f9f3315fa4b831e93c36cd88196480 SP:Human @SQ SN:chrUn_KI270394v1 LN:970 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:d5171e863a3d8f832f0559235987b1e5 SP:Human @SQ SN:chrUn_KI270386v1 LN:1788 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:b9b1baaa7abf206f6b70cf31654172db SP:Human @SQ SN:chrUn_KI270391v1 LN:1484 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:1fa5cf03b3eac0f1b4a64948fd09de53 SP:Human @SQ SN:chrUn_KI270383v1 LN:1750 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:694d75683e4a9554bcc1291edbcaee43 SP:Human @SQ SN:chrUn_KI270393v1 LN:1308 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:3724e1d70677d6b5c4bcf17fd40da111 SP:Human @SQ SN:chrUn_KI270384v1 LN:1658 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:b06e44ea15d0a57618d6ca7d2e6ac5d2 SP:Human @SQ SN:chrUn_KI270392v1 LN:971 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:59b3ca8de65fb171683f8a06d3b4bf0d SP:Human @SQ SN:chrUn_KI270381v1 LN:1930 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:2a9297cfd3b3807195ab9ad07e775d99 SP:Human @SQ SN:chrUn_KI270385v1 LN:990 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:112a8b1df94ef0498a0bfe2d2ea5cc23 SP:Human @SQ SN:chrUn_KI270382v1 LN:4215 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:e7085cdcee6ad62f359744e13d3209fc SP:Human @SQ SN:chrUn_KI270376v1 LN:1136 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:59e8fc80b78d62325082334b43dffdba SP:Human @SQ SN:chrUn_KI270374v1 LN:2656 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:dbc92c9a92e558946e58b4909ec95dd5 SP:Human @SQ SN:chrUn_KI270372v1 LN:1650 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:53a9d5e8fd28bce5da5efcfd9114dbf2 SP:Human @SQ SN:chrUn_KI270373v1 LN:1451 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:b174fe53be245a840cd6324e39b88ced SP:Human @SQ SN:chrUn_KI270375v1 LN:2378 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:d678250c97e9b94aa390fa46e70a6d83 SP:Human @SQ SN:chrUn_KI270371v1 LN:2805 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:a0af3d778dfeb7963e8e6d84c0c54fba SP:Human @SQ SN:chrUn_KI270448v1 LN:7992 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:0f40827c265cb813b6e723da6c9b926b SP:Human @SQ SN:chrUn_KI270521v1 LN:7642 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:af5bef7cefec7bd7efa729ac6c5be088 SP:Human @SQ SN:chrUn_GL000195v1 LN:182896 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:5d9ec007868d517e73543b005ba48535 SP:Human @SQ SN:chrUn_GL000219v1 LN:179198 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Human @SQ SN:chrUn_GL000220v1 LN:161802 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:fc35de963c57bf7648429e6454f1c9db SP:Human @SQ SN:chrUn_GL000224v1 LN:179693 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Human @SQ SN:chrUn_KI270741v1 LN:157432 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:86eaea8a15a3950e37442eaaa5c9dc92 SP:Human @SQ SN:chrUn_GL000226v1 LN:15008 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Human @SQ SN:chrUn_GL000213v1 LN:164239 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:9d424fdcc98866650b58f004080a992a SP:Human @SQ SN:chrUn_KI270743v1 LN:210658 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:3b62d9d3100f530d509e4efebd98502c SP:Human @SQ SN:chrUn_KI270744v1 LN:168472 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:e90aee46b947ff8c32291a6843fde3f9 SP:Human @SQ SN:chrUn_KI270745v1 LN:41891 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:1386fe3de6f82956f2124e19353ff9c1 SP:Human @SQ SN:chrUn_KI270746v1 LN:66486 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:c470486a0a858e14aa21d7866f83cc17 SP:Human @SQ SN:chrUn_KI270747v1 LN:198735 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:62375d812ece679c9fd2f3d08d4e22a4 SP:Human @SQ SN:chrUn_KI270748v1 LN:93321 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:4f6c6ab005c852a4352aa33e7cc88ded SP:Human @SQ SN:chrUn_KI270749v1 LN:158759 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:c899a7b4e911d371283f3f4058ca08b7 SP:Human @SQ SN:chrUn_KI270750v1 LN:148850 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:c022ba92f244b7dc54ea90c4eef4d554 SP:Human @SQ SN:chrUn_KI270751v1 LN:150742 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:1b758bbdee0e9ca882058d916cba9d29 SP:Human @SQ SN:chrUn_KI270752v1 LN:27745 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:e0880631848337bd58559d9b1519da63 SP:Human @SQ SN:chrUn_KI270753v1 LN:62944 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:25075fb2a1ecada67c0eb2f1fe0c7ec9 SP:Human @SQ SN:chrUn_KI270754v1 LN:40191 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:fe9e16233cecbc244f06f3acff3d03b8 SP:Human @SQ SN:chrUn_KI270755v1 LN:36723 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:4a7da6a658955bd787af8add3ccb5751 SP:Human @SQ SN:chrUn_KI270756v1 LN:79590 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:2996b120a5a5e15dab6555f0bf92e374 SP:Human @SQ SN:chrUn_KI270757v1 LN:71251 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:174c73b60b41d8a1ef0fbaa4b3bdf0d3 SP:Human @SQ SN:chrUn_GL000214v1 LN:137718 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:46c2032c37f2ed899eb41c0473319a69 SP:Human @SQ SN:chrUn_KI270742v1 LN:186739 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:2f31c013a4a8301deb8ab7ed1ca1cd99 SP:Human @SQ SN:chrUn_GL000216v2 LN:176608 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:725009a7e3f5b78752b68afa922c090c SP:Human @SQ SN:chrUn_GL000218v1 LN:161147 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:1d708b54644c26c7e01c2dad5426d38c SP:Human @SQ SN:chrEBV LN:171823 UR:/lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa AS:GRCh38 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Human @RG ID:23847_8#14 PL:ILLUMINA PU:170925_HS33_23847_B_CBCU2ANXX_8#14 LB:20046769 DS:EGAS00001001755: In this study we will compare the single cell transcriptomes of immune cells from asthmatics responding to steroids, those refractory to steroids, and a control population. 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:2017-09-25T01:00:00+0100 PG:SCS SM:CTTV027_RNAseq7095608 CN:SC @PG ID:SCS PN:RTA VN:1.18.66.3 DS:Controlling software on instrument @PG ID:basecalling PN:RTA PP:SCS VN:1.18.66.3 DS:Basecalling Package @PG ID:bambi PN:bambi PP:basecalling VN:0.9.11 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.11/bin/bambi i2b --intensity-dir=/nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities --basecalls-dir=/nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BaseCalls --lane=8 --platform-unit=170925_HS33_23847_B_CBCU2ANXX_8 --read-group-id=23847_8 --study-name="EGAS00001001755: In this study we will compare the single cell transcriptomes of immune cells from asthmatics responding to steroids, those refractory to steroids, and a control population. 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/" 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q7095821,CTTV027_RNAseq7095822,CTTV027_RNAseq7095823,CTTV027_RNAseq7095824,CTTV027_RNAseq7095825,CTTV027_RNAseq7095826,CTTV027_RNAseq7095827,CTTV027_RNAseq7095828,CTTV027_RNAseq7095829,CTTV027_RNAseq7095830,CTTV027_RNAseq7095831,CTTV027_RNAseq7095832,CTTV027_RNAseq7095833,CTTV027_RNAseq7095834,CTTV027_RNAseq7095835,CTTV027_RNAseq7095836,CTTV027_RNAseq7095837,CTTV027_RNAseq7095838,CTTV027_RNAseq7095839,CTTV027_RNAseq7095840,CTTV027_RNAseq7095841,CTTV027_RNAseq7095842,CTTV027_RNAseq7095843,CTTV027_RNAseq7095844,CTTV027_RNAseq7095845,CTTV027_RNAseq7095846,CTTV027_RNAseq7095847,CTTV027_RNAseq7095848,CTTV027_RNAseq7095849,CTTV027_RNAseq7095850,CTTV027_RNAseq7095851,CTTV027_RNAseq7095852,CTTV027_RNAseq7095853,CTTV027_RNAseq7095854,CTTV027_RNAseq7095855,CTTV027_RNAseq7095856,CTTV027_RNAseq7095857,CTTV027_RNAseq7095858,CTTV027_RNAseq7095859,CTTV027_RNAseq7095860,CTTV027_RNAseq7095861,CTTV027_RNAseq7095862,CTTV027_RNAseq7095863,CTTV027_RNAseq7095864,CTTV027_RNAseq7095865,CTTV027_RNAseq7095866,CTTV027_RNAseq7095867,CTTV027_RNAseq7095868,CTTV027_RNAseq7095869,CTTV027_RNAseq7095870,CTTV027_RNAseq7095871,CTTV027_RNAseq7095872,CTTV027_RNAseq7095873,CTTV027_RNAseq7095874,CTTV027_RNAseq7095875,CTTV027_RNAseq7095876,CTTV027_RNAseq7095877,CTTV027_RNAseq7095878,CTTV027_RNAseq7095879,CTTV027_RNAseq7095880,CTTV027_RNAseq7095881,CTTV027_RNAseq7095882 --output-file=- --compression-level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:bambi VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamadapterfind level=0 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.9.11 CL:/software/solexa/pkg/bambi/0.9.11/bin/bambi decode --metrics-file /nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/23847_8.bam.tag_decode.metrics --barcode-file /nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/metadata_cache_23847/lane_8.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 PP:bambi.1 VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamcollate2 collate=2 level=0 @PG ID:bwa PN:bwa PP:bamcollate2 VN:0.7.16a-r1181 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/yxO_ARx9i0/alnphix_bwa_aln_1_out /tmp/zfihe0JoKv/alnphix_bwa_aln_2_out /tmp/lhEtT5jQX1/alnphix_simple_cat1_out /tmp/35OUBW4QJs/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 2 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/W_VvS5dkeT/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:v10.28-dirty CL:/software/solexa/pkg/pb_calibration/10.28/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/no_cal/archive/qc/tileviz/23847_8 --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/10.28/bin/spatial_filter -a -f -u -l /nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/no_cal/23847_8.bam.filter.stats -F /tmp/CNBhHBs6Pj/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.5 CL:/software/solexa/pkg/samtools/1.5/bin/samtools split -f /nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/no_cal/lane8/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 PP:samtools VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamcollate2 collate=1 level=0 @PG ID:bamreset PN:bamreset PP:bamcollate2' VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamreset resetaux=0 level=0 verbose=0 @PG ID:bamadapterclip PN:bamadapterclip PP:bamreset VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamadapterclip verbose=0 level=0 @PG ID:bwa' PN:bwa PP:bamadapterclip VN:0.7.16a-r1181 CL:/software/solexa/pkg/bwa/0.7.16a/bwa mem -t 8 -p -Y -K 100000000 /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/bwa0_6/Homo_sapiens.GRCh38_15.fa /tmp/vQbJTxEAU5/alntgt_bamtofastq_out @PG ID:scramble' PN:scramble PP:bwa' VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -I sam -O bam @PG ID:samtools' PN:samtools PP:scramble' VN:1.5 CL:/software/solexa/pkg/samtools/1.5/bin/samtools reheader /tmp/skld2LNnl6/postalntgt_alterSQ_headerSQfix_out /tmp/Ff_UAqKGu8/postalntgt_mbuffer_headerSQfix_out @PG ID:bam12split PN:bam12split PP:samtools' VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bam12split verbose=0 level=0 @PG ID:bamsormadup PN:bamsormadup PP:bam12split VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamsormadup threads=8 SO=queryname level=0 @PG ID:bam12auxmerge' PN:bam12auxmerge PP:bamsormadup VN:2.0.76 CL:/software/solexa/pkg/biobambam/2.0.76/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/7OWwjvrT8u/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_23847_8#14.bam, /tmp/rz_UIh9wFF/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/rtIMl8agfe/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=23847_8#14.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/2.0.76/bin/bamsormadup threads=8 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/no_cal/archive/lane8/bsfopt_23847_8#14.tmp PP:AlignmentFilter VN:2.0.76 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.76/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/no_cal/archive/lane8/bmdfopt_23847_8#14.tmp M=/nfs/sf46/ILorHSany_sf46/analysis/170925_HS33_23847_B_CBCU2ANXX/Data/Intensities/BAM_basecalls_20170929-164501/no_cal/archive/lane8/23847_8#14.markdups_metrics.txt PP:bamsormadup' VN:2.0.76 @PG ID:scramble.3 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -t 3 -7 -I bam -O cram -r /lustre/scratch117/core/sciops_repository/references/Homo_sapiens/GRCh38_15/all/fasta/Homo_sapiens.GRCh38_15.fa @CO TY:checksum ST:all PA:all HA:crc32prod CO:1893240 BS:60d3139e NS:68ad145c SQ:17caa9cf ST:BC,FI,QT,RT,TC:1833bfa6 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:1893120 BS:2d590fb8 NS:432bd498 SQ:7d911bcd ST:BC,FI,QT,RT,TC:5b7fac88 @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:23847_8#14 PA:all HA:crc32prod CO:1893240 BS:60d3139e NS:68ad145c SQ:17caa9cf ST:BC,FI,QT,RT,TC:1833bfa6 @CO TY:checksum ST:23847_8#14 PA:pass HA:crc32prod CO:1893120 BS:2d590fb8 NS:432bd498 SQ:7d911bcd ST:BC,FI,QT,RT,TC:5b7fac88