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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 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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:25467_3#76 DT:2018-03-20T00:00:00+0000 PU:180320_HS36_25467_A_CC7WFANXX_3#76 LB:20382181 PG:SCS SM:I1147 CN:SC PL:ILLUMINA DS:EGAS00001002813: Gene regulation of human CD4+ Treg cells 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/ @PG ID:SCS VN:1.18.66.3 PN:RTA DS:Controlling software on instrument @PG ID:basecalling PP:SCS VN:1.18.66.3 PN:RTA DS:Basecalling Package @PG ID:bambi PP:basecalling VN:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi i2b --intensity-dir=/nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities --basecalls-dir=/nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BaseCalls --lane=3 --platform-unit=180320_HS36_25467_A_CC7WFANXX_3 --read-group-id=25467_3 --study-name="EGAS00001002813: Gene regulation of human CD4+ Treg cells 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=I1121,I1129,I1137,I1145,I1153,I1161,I1169,I1193,I1201,I1209,I1177,I1185,I1122,I1130,I1138,I1146,I1154,I1162,I1170,I1194,I1202,I1210,I1178,I1186,I1124,I1132,I1140,I1148,I1156,I1164,I1172,I1196,I1204,I1212,I1180,I1188,I1125,I1133,I1141,I1149,I1157,I1165,I1173,I1197,I1205,I1213,I1181,I1189,I1126,I1134,I1142,I1150,I1158,I1166,I1174,I1198,I1206,I1214,I1182,I1190,I1127,I1135,I1143,I1151,I1159,I1167,I1175,I1199,I1207,I1215,I1183,I1191,I1123,I1131,I1139,I1147,I1155,I1163,I1171,I1195,I1203,I1211,I1179,I1187,I1120,I1128,I1136,I1144,I1152,I1160,I1168,I1192,I1200,I1208,I1176,I1184 --threads=3 --output-file=- --compression-level=0 PN:bambi DS:Convert Illumina BCL to BAM or SAM file @PG ID:bamadapterfind PN:bamadapterfind CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamadapterfind level=0 PP:bambi VN:2.0.79 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi decode --metrics-file /nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/25467_3.bam.tag_decode.metrics --barcode-file /nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/metadata_cache_25467/lane_3.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamcollate2 collate=2 level=0 PP:bambi.1 VN:2.0.79 @PG ID:bwa PN:bwa 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/1Qy0CeEuHQ/alnphix_bwa_aln_1_out /tmp/x7INSI20E1/alnphix_bwa_aln_2_out /tmp/M7ZgTooD_j/alnphix_simple_cat1_out /tmp/VIFjr4XO88/alnphix_simple_cat2_out PP:bamcollate2 VN:0.7.16a-r1181 @PG ID:scramble PN:scramble CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -t 2 -I sam -O bam PP:bwa VN:1.14.9 @PG ID:bam12auxmerge PN:bam12auxmerge CL:/software/solexa/pkg/biobambam/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/zKaESVeLI5/simple_cat_out PP:scramble VN:2.0.79 @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:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi spatial_filter -c -t /nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/no_cal/archive/qc/tileviz/25467_3 -F /dev/stdout /dev/stdin ; /software/solexa/pkg/bambi/0.10.1/bin/bambi spatial_filter -a --compression-level 0 -f -F /tmp/krfYm0KvN6/tee_post_filter_creation:__APPLY_FILTER_OUT___out -l /nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/no_cal/25467_3.bam.filter.stats /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.6 CL:/software/solexa/pkg/samtools/1.6/bin/samtools split -f /nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/no_cal/lane3/%!.bam - @PG ID:bamcollate2' PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamcollate2 collate=1 level=0 PP:samtools VN:2.0.79 @PG ID:bamreset PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamreset resetaux=0 level=0 verbose=0 PP:bamcollate2' VN:2.0.79 @PG ID:bamadapterclip PN:bamadapterclip CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamadapterclip verbose=0 level=0 PP:bamreset VN:2.0.79 @PG ID:bwa' PN:bwa 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/70hE3E_ZQk/aln_alntgt_bamtofastq_out PP:bamadapterclip VN:0.7.16a-r1181 @PG ID:scramble' PN:scramble CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -I sam -O bam PP:bwa' VN:1.14.9 @PG ID:samtools' PN:samtools CL:/software/solexa/pkg/samtools/1.6/bin/samtools reheader /tmp/W2kpKhZpXp/aln_postaln_alterSQ_headerSQfix_out /tmp/If_RFffnaA/aln_postaln_mbuffer_headerSQfix_out PP:scramble' VN:1.6 @PG ID:bam12split PN:bam12split CL:/software/solexa/pkg/biobambam/2.0.79/bin/bam12split verbose=0 level=0 PP:samtools' VN:2.0.79 @PG ID:bam12auxmerge' PN:bam12auxmerge CL:/software/solexa/pkg/biobambam/2.0.79/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 /tmp/YNcEJ4ss_d/aln_amp_bamadapterclip_pre_auxmerge_out PP:bam12split VN:2.0.79 @PG ID:bambi.2 PN:bambi PP:bam12auxmerge' VN:0.10.1 CL:/software/solexa/pkg/bambi/0.10.1/bin/bambi select --compression-level 0 --input /tmp/3g5ZtAoba4/aln_tee3_tee3:to_phix_aln_out,/tmp/V5GU0J_g_C/aln_bam12auxmerge_out --output /tmp/OdgWTll5u0/alignment_filter:phix_bam_out_out,/tmp/iyleW7_t4E/alignment_filter:target_bam_out_out -m 25467_3#76.bam_alignment_filter_metrics.json DS:Split alignments into different files @PG ID:bamsormadup PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamsormadup threads=8 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/no_cal/archive/lane3/bsfopt_25467_3#76.tmp PP:bambi.2 VN:2.0.79 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/no_cal/archive/lane3/bmdfopt_25467_3#76.tmp M=/nfs/sf31/ILorHSany_sf31/analysis/180320_HS36_25467_A_CC7WFANXX/Data/Intensities/BAM_basecalls_20180324-090011/no_cal/archive/lane3/25467_3#76.markdups_metrics.txt PP:bamsormadup VN:2.0.79 @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:2986970 BS:52a654ab NS:61fb89ab SQ:59fcccb0 ST:BC,FI,QT,RT,TC:1ad2dd35 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:2986970 BS:52a654ab NS:61fb89ab SQ:59fcccb0 ST:BC,FI,QT,RT,TC:1ad2dd35 @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:25467_3#76 PA:all HA:crc32prod CO:2986970 BS:52a654ab NS:61fb89ab SQ:59fcccb0 ST:BC,FI,QT,RT,TC:1ad2dd35 @CO TY:checksum ST:25467_3#76 PA:pass HA:crc32prod CO:2986970 BS:52a654ab NS:61fb89ab SQ:59fcccb0 ST:BC,FI,QT,RT,TC:1ad2dd35