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UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Human @SQ SN:GL000214.1 LN:137718 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:46c2032c37f2ed899eb41c0473319a69 SP:Human @SQ SN:GL000221.1 LN:155397 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:3238fb74ea87ae857f9c7508d315babb SP:Human @SQ SN:GL000209.1 LN:159169 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Human @SQ SN:GL000218.1 LN:161147 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Human @SQ SN:GL000220.1 LN:161802 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:fc35de963c57bf7648429e6454f1c9db SP:Human @SQ SN:GL000213.1 LN:164239 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:9d424fdcc98866650b58f004080a992a SP:Human @SQ SN:GL000211.1 LN:166566 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Human @SQ SN:GL000199.1 LN:169874 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:569af3b73522fab4b40995ae4944e78e SP:Human @SQ SN:GL000217.1 LN:172149 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Human @SQ SN:GL000216.1 LN:172294 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:642a232d91c486ac339263820aef7fe0 SP:Human @SQ SN:GL000215.1 LN:172545 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:5eb3b418480ae67a997957c909375a73 SP:Human @SQ SN:GL000205.1 LN:174588 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Human @SQ SN:GL000219.1 LN:179198 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Human @SQ SN:GL000224.1 LN:179693 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Human @SQ SN:GL000223.1 LN:180455 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Human @SQ SN:GL000195.1 LN:182896 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:5d9ec007868d517e73543b005ba48535 SP:Human @SQ SN:GL000212.1 LN:186858 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:563531689f3dbd691331fd6c5730a88b SP:Human @SQ SN:GL000222.1 LN:186861 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Human @SQ SN:GL000200.1 LN:187035 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Human @SQ SN:GL000193.1 LN:189789 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Human @SQ SN:GL000194.1 LN:191469 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Human @SQ SN:GL000225.1 LN:211173 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:63945c3e6962f28ffd469719a747e73c SP:Human @SQ SN:GL000192.1 LN:547496 UR:/tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/cwd/24252_5#370/../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Human @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:0.9.12 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.12/bin/bambi i2b --intensity-dir=/nfs/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities --basecalls-dir=/nfs/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BaseCalls --lane=5 --platform-unit=171103_HS37_24252_A_CBN3WANXX_5 --read-group-id=24252_5 --study-name="EGAS00001002278: When comparing the differentiation capacities of pluripotent stem cell lines that have different genetic backgrounds, batch to batch experimental variablility poses a significant challenge, especially when trying to identify smaller effects. One way to address this issue is to differentiate several different lines in the same culture dish, thereby elimating experimental variation. In addition, it allows researchers to analyze many more lines with less experiments. Parallel single cell RNA-Seq exploits that individual cells are tagged and hence each cell can be reliably assigned to the donor of origin based on the genetic variants it contains. In addition, analyzing the genetic signature of single cells within a differentiating population can reveal differentation stages that are not easily detected in bulk RNAseq data. 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=4636STDY7165299,4636STDY7165300,4636STDY7165301,4636STDY7165302,4636STDY7165303,4636STDY7165304,4636STDY7165305,4636STDY7165306,4636STDY7165307,4636STDY7165308,4636STDY7165309,4636STDY7165310,4636STDY7165311,4636STDY7165312,4636STDY7165313,4636STDY7165314,4636STDY7165315,4636STDY7165316,4636STDY7165317,4636STDY7165318,4636STDY7165319,4636STDY7165320,4636STDY7165321,4636STDY7165322,4636STDY7165323,4636STDY7165324,4636STDY7165325,4636STDY7165326,4636STDY7165327,4636STDY7165328,4636STDY7165329,4636STDY7165330,4636STDY7165331,4636STDY7165332,4636STDY7165333,4636STDY7165334,4636STDY7165335,4636STDY7165336,4636STDY7165337,4636STDY7165338,4636STDY7165339,4636STDY7165340,4636STDY7165341,4636STDY7165342,4636STDY7165343,4636STDY7165344,4636STDY7165345,4636STDY7165346,4636STDY7165347,4636STDY7165348,4636STDY7165349,4636STDY7165350,4636STDY7165351,4636STDY7165352,4636STDY7165353,4636STDY7165354,4636STDY7165355,4636STDY7165356,4636STDY7165357,4636STDY7165358,4636STDY7165359,4636STDY7165360,4636STDY7165361,4636STDY7165362,4636STDY7165363,4636STDY7165364,4636STDY7165365,4636STDY7165366,4636STDY7165367,4636STDY7165368,4636STDY7165369,4636STDY7165370,4636STDY7165371,4636STDY7165372,4636STDY7165373,4636STDY7165374,4636STDY7165375,4636STDY7165376,4636STDY7165377,4636STDY7165378,4636STDY7165379,4636STDY7165380,4636STDY7165381,4636STDY7165382,4636STDY7165383,4636STDY7165384,4636STDY7165385,4636STDY7165386,4636STDY7165387,4636STDY7165388,4636STDY7165389,4636STDY7165390,4636STDY7165391,4636STDY7165392,4636STDY7165393,4636STDY7165394,4636STDY7165395,4636STDY7165396,4636STDY7165397,4636STDY7165398,4636STDY7165399,4636STDY7165400,4636STDY7165401,4636STDY7165402,4636STDY7165403,4636STDY7165404,4636STDY7165405,4636STDY7165406,4636STDY7165407,4636STDY7165408,4636STDY7165409,4636STDY7165410,4636STDY7165411,4636STDY7165412,4636STDY7165413,4636STDY7165414,4636STDY7165415,4636STDY7165416,4636STDY7165417,4636STDY7165418,4636STDY7165419,4636STDY7165420,4636STDY7165421,4636STDY7165422,4636STDY7165423,4636STDY7165424,4636STDY7165425,4636STDY7165426,4636STDY7165427,4636STDY7165428,4636STDY7165429,4636STDY7165430,4636STDY7165431,4636STDY7165432,4636STDY7165433,4636STDY7165434,4636STDY7165435,4636STDY7165436,4636STDY7165437,4636STDY7165438,4636STDY7165439,4636STDY7165440,4636STDY7165441,4636STDY7165442,4636STDY7165443,4636STDY7165444,4636STDY7165445,4636STDY7165446,4636STDY7165447,4636STDY7165448,4636STDY7165449,4636STDY7165450,4636STDY7165451,4636STDY7165452,4636STDY7165453,4636STDY7165454,4636STDY7165455,4636STDY7165456,4636STDY7165457,4636STDY7165458,4636STDY7165459,4636STDY7165460,4636STDY7165461,4636STDY7165462,4636STDY7165463,4636STDY7165464,4636STDY7165465,4636STDY7165466,4636STDY7165467,4636STDY7165468,4636STDY7165469,4636STDY7165470,4636STDY7165471,4636STDY7165472,4636STDY7165473,4636STDY7165474,4636STDY7165475,4636STDY7165476,4636STDY7165477,4636STDY7165478,4636STDY7165479,4636STDY7165480,4636STDY7165481,4636STDY7165482,4636STDY7165483,4636STDY7165484,4636STDY7165485,4636STDY7165486,4636STDY7165487,4636STDY7165488,4636STDY7165489,4636STDY7165490,4636STDY7165491,4636STDY7165492,4636STDY7165493,4636STDY7165494,4636STDY7165495,4636STDY7165496,4636STDY7165497,4636STDY7165498,4636STDY7165499,4636STDY7165500,4636STDY7165501,4636STDY7165502,4636STDY7165503,4636STDY7165504,4636STDY7165505,4636STDY7165506,4636STDY7165507,4636STDY7165508,4636STDY7165509,4636STDY7165510,4636STDY7165511,4636STDY7165512,4636STDY7165513,4636STDY7165514,4636STDY7165515,4636STDY7165516,4636STDY7165517,4636STDY7165518,4636STDY7165519,4636STDY7165520,4636STDY7165521,4636STDY7165522,4636STDY7165523,4636STDY7165524,4636STDY7165525,4636STDY7165526,4636STDY7165527,4636STDY7165528,4636STDY7165529,4636STDY7165530,4636STDY7165531,4636STDY7165532,4636STDY7165533,4636STDY7165534,4636STDY7165535,4636STDY7165536,4636STDY7165537,4636STDY7165538,4636STDY7165539,4636STDY7165540,4636STDY7165541,4636STDY7165542,4636STDY7165543,4636STDY7165544,4636STDY7165545,4636STDY7165546,4636STDY7165547,4636STDY7165548,4636STDY7165549,4636STDY7165550,4636STDY7165551,4636STDY7165552,4636STDY7165553,4636STDY7165554,4636STDY7165555,4636STDY7165556,4636STDY7165557,4636STDY7165558,4636STDY7165559,4636STDY7165560,4636STDY7165561,4636STDY7165562,4636STDY7165563,4636STDY7165564,4636STDY7165565,4636STDY7165566,4636STDY7165567,4636STDY7165568,4636STDY7165569,4636STDY7165570,4636STDY7165571,4636STDY7165572,4636STDY7165573,4636STDY7165574,4636STDY7165575,4636STDY7165576,4636STDY7165577,4636STDY7165578,4636STDY7165579,4636STDY7165580,4636STDY7165581,4636STDY7165582,4636STDY7165583,4636STDY7165584,4636STDY7165585,4636STDY7165586,4636STDY7165587,4636STDY7165588,4636STDY7165589,4636STDY7165590,4636STDY7165591,4636STDY7165592,4636STDY7165593,4636STDY7165594,4636STDY7165595,4636STDY7165596,4636STDY7165597,4636STDY7165598,4636STDY7165599,4636STDY7165600,4636STDY7165601,4636STDY7165602,4636STDY7165603,4636STDY7165604,4636STDY7165605,4636STDY7165606,4636STDY7165607,4636STDY7165608,4636STDY7165609,4636STDY7165610,4636STDY7165611,4636STDY7165612,4636STDY7165613,4636STDY7165614,4636STDY7165615,4636STDY7165616,4636STDY7165617,4636STDY7165618,4636STDY7165619,4636STDY7165620,4636STDY7165621,4636STDY7165622,4636STDY7165623,4636STDY7165624,4636STDY7165625,4636STDY7165626,4636STDY7165627,4636STDY7165628,4636STDY7165629,4636STDY7165630,4636STDY7165631,4636STDY7165632,4636STDY7165633,4636STDY7165634,4636STDY7165635,4636STDY7165636,4636STDY7165637,4636STDY7165638,4636STDY7165639,4636STDY7165640,4636STDY7165641,4636STDY7165642,4636STDY7165643,4636STDY7165644,4636STDY7165645,4636STDY7165646,4636STDY7165647,4636STDY7165648,4636STDY7165649,4636STDY7165650,4636STDY7165651,4636STDY7165652,4636STDY7165653,4636STDY7165654,4636STDY7165655,4636STDY7165656,4636STDY7165657,4636STDY7165658,4636STDY7165659,4636STDY7165660,4636STDY7165661,4636STDY7165662,4636STDY7165663,4636STDY7165664,4636STDY7165665,4636STDY7165666,4636STDY7165667,4636STDY7165668,4636STDY7165669,4636STDY7165670,4636STDY7165671,4636STDY7165672,4636STDY7165673,4636STDY7165674,4636STDY7165675,4636STDY7165676,4636STDY7165677,4636STDY7165678,4636STDY7165679,4636STDY7165680,4636STDY7165681,4636STDY7165682 --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:0.9.12 CL:/software/solexa/pkg/bambi/0.9.12/bin/bambi decode --metrics-file /nfs/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/24252_5.bam.tag_decode.metrics --barcode-file /nfs/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/metadata_cache_24252/lane_5.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/q7GaGYXUfN/alnphix_bwa_aln_1_out /tmp/VU4BqsDrCo/alnphix_bwa_aln_2_out /tmp/e8PVzFDQZq/alnphix_simple_cat1_out /tmp/N21H445VQ8/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/_yRv2OteOq/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/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/no_cal/archive/qc/tileviz/24252_5 --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/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/no_cal/24252_5.bam.filter.stats -F /tmp/ogYYzX87Lh/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.6 CL:/software/solexa/pkg/samtools/1.6/bin/samtools split -f /nfs/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/no_cal/lane5/%!.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/1000Genomes/all/bwa0_6/human_g1k_v37.fasta /tmp/v_b2Ba1fYu/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:1.6 CL:/software/solexa/pkg/samtools/1.6/bin/samtools reheader /tmp/HAHGPZ1t0a/postalntgt_alterSQ_headerSQfix_out /tmp/Gf1L1RvrHe/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/EEGJ0bJg2H/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_24252_5#370.bam, /tmp/SIPODhgjgW/postalntgt_bam12auxmerge_out] OUTPUT_ALIGNMENT=[/tmp/bC3q_N04H0/alignment_filter:__PHIX_BAM_OUT___out, /dev/stdout] METRICS_FILE=24252_5#370.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/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/no_cal/archive/lane5/bsfopt_24252_5#370.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/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/no_cal/archive/lane5/bmdfopt_24252_5#370.tmp M=/nfs/sf53/ILorHSany_sf53/analysis/171103_HS37_24252_A_CBN3WANXX/Data/Intensities/BAM_basecalls_20171108-221948/no_cal/archive/lane5/24252_5#370.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/1000Genomes/all/fasta/human_g1k_v37.fasta @PG ID:bamcollate2'' PN:bamcollate2 CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamcollate2 inputformat=cram collate=1 level=0 PP:scramble.3 VN:2.0.79 @PG ID:bamreset' PN:bamreset CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamreset resetaux=0 auxfilter=RG,PG,BC,RT,QT,tr,tq,br,qr level=0 verbose=0 PP:bamcollate2'' VN:2.0.79 @PG ID:bamadapterfind' PN:bamadapterfind CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamadapterfind clip=1 verbose=0 level=0 PP:bamreset' VN:2.0.79 @PG ID:bwa'' PN:bwa CL:/software/solexa/pkg/bwa/0.7.17/bwa mem -t 16 -p -Y -K 100000000 ../npg-repository/references/Homo_sapiens/1000Genomes/all/bwa0_6/human_g1k_v37.fasta /tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/tmp/QgYJSsFjX3/alntgt_bamtofastq_out PP:bamadapterfind' VN:0.7.17-r1188 @PG ID:scramble'' PN:scramble CL:/software/solexa/pkg/staden_io_lib/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/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/tmp/9mnc4T0WbV/postalntgt_alterSQ_headerSQfix_out /tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/tmp/gIJtCgAfjn/postalntgt_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:bamsormadup'' PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamsormadup threads=16 SO=queryname level=0 PP:bam12split' 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/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/tmp/49WgVp8KuI/amp_bamadapterclip_pre_auxmerge_out PP:bamsormadup'' VN:2.0.79 @PG ID:bambi.2 PN:bambi PP:bam12auxmerge'' OT:TARGET VN:0.10.0 CL:/software/solexa/pkg/bambi/0.10.0/bin/bambi chrsplit --exclude /tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/tmp/1F__zMAAkY/foptgt_split:__SPLIT_OUT___out --input /tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/tmp/hfV6e9V6Df/postalntgt_bam12auxmerge_out --output /tmp/wr_cwd/1/5/6/60d9a92e6d078bcf4ac91243e4cfc054461428/tmp/zosOlQRRnR/foptgt_split:__TARGET_OUT___out --subset Y --invert DS:Split BAM file by chromosomes @PG ID:bamsormadup''' PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.79/bin/bamsormadup threads=16 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=out/bspaft_24252_5#370.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=out/bmdpaft_24252_5#370.tmp M=out/24252_5#370.markdups_metrics.txt PP:bamsormadup''' VN:2.0.79 @PG ID:scramble.4 PN:scramble PP:bamstreamingmarkduplicates' VN:1.14.9 CL:/software/solexa/pkg/staden_io_lib/1.14.9/bin/scramble -7 -I bam -O cram -r ../npg-repository/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta @RG ID:24252_5#370 PL:ILLUMINA PU:171103_HS37_24252_A_CBN3WANXX_5#370 LB:20339735 DS:EGAS00001002278: When comparing the differentiation capacities of pluripotent stem cell lines that have different genetic backgrounds, batch to batch experimental variablility poses a significant challenge, especially when trying to identify smaller effects. One way to address this issue is to differentiate several different lines in the same culture dish, thereby elimating experimental variation. In addition, it allows researchers to analyze many more lines with less experiments. Parallel single cell RNA-Seq exploits that individual cells are tagged and hence each cell can be reliably assigned to the donor of origin based on the genetic variants it contains. In addition, analyzing the genetic signature of single cells within a differentiating population can reveal differentation stages that are not easily detected in bulk RNAseq data. 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:2017-11-03T00:00:00+0000 PG:SCS SM:4636STDY7165668 CN:SC @CO TY:checksum ST:all PA:all HA:crc32prod CO:1073164 BS:3befd057 NS:3c655627 SQ:193012b9 ST:BC,FI,QT,RT,TC:74a1a512 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:1073072 BS:5c8cdbe0 NS:6661f6f5 SQ:85e8a05 ST:BC,FI,QT,RT,TC:71411f24 @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:24252_5#370 PA:all HA:crc32prod CO:1073164 BS:3befd057 NS:3c655627 SQ:193012b9 ST:BC,FI,QT,RT,TC:74a1a512 @CO TY:checksum ST:24252_5#370 PA:pass HA:crc32prod CO:1073072 BS:5c8cdbe0 NS:6661f6f5 SQ:85e8a05 ST:BC,FI,QT,RT,TC:71411f24