@HD VN:1.4 SO:coordinate @RG ID:1#71 PL:ILLUMINA PU:141124_MS3_14786_A_MS2775046-500V2_1#71 LB:12396923 DS:EGAS00001000814: The aim of this study is to ascertain whether leukaemic mutations exist within the blood of people with otherwise normal haematopoeisis. To satisfy this aim we plan to look for 7 known leukaemic mutations in the whole blood DNA of a large cohort of blood donors who have normal haematopoesis. Genomic regions around mutational sites have been amplified using a 2 step PCR process which involves barcoding of individual patients DT:2014-11-24T00:00:00+0000 SM:EGAN00001249156 PG:BamIndexDecoder CN:SC @PG ID:SCS PN:MiSeq Control Software DS:Controlling software on instrument VN:2.5.0.5 @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.18.54.0 @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.16 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001249086,EGAN00001249087,EGAN00001249088,EGAN00001249089,EGAN00001249090,EGAN00001249091,EGAN00001249092,EGAN00001249093,EGAN00001249094,EGAN00001249095,EGAN00001249096,EGAN00001249097,EGAN00001249098,EGAN00001249099,EGAN00001249100,EGAN00001249101,EGAN00001249102,EGAN00001249103,EGAN00001249104,EGAN00001249105,EGAN00001249106,EGAN00001249107,EGAN00001249108,EGAN00001249109,EGAN00001249110,EGAN00001249111,EGAN00001249112,EGAN00001249113,EGAN00001249114,EGAN00001249115,EGAN00001249116,EGAN00001249117,EGAN00001249118,EGAN00001249119,EGAN00001249120,EGAN00001249121,EGAN00001249122,EGAN00001249123,EGAN00001249124,EGAN00001249125,EGAN00001249126,EGAN00001249127,EGAN00001249128,EGAN00001249129,EGAN00001249130,EGAN00001249131,EGAN00001249132,EGAN00001249133,EGAN00001249134,EGAN00001249135,EGAN00001249136,EGAN00001249137,EGAN00001249138,EGAN00001249139,EGAN00001249140,EGAN00001249141,EGAN00001249142,EGAN00001249143,EGAN00001249144,EGAN00001249145,EGAN00001249146,EGAN00001249147,EGAN00001249148,EGAN00001249149,EGAN00001249150,EGAN00001249151,EGAN00001249152,EGAN00001249153,EGAN00001249154,EGAN00001249155,EGAN00001249156,EGAN00001249157,EGAN00001249158,EGAN00001249159,EGAN00001249160,EGAN00001249161,EGAN00001249162,EGAN00001249163,EGAN00001249164,EGAN00001249165,EGAN00001249166,EGAN00001249167,EGAN00001249168,EGAN00001249169,EGAN00001249170,EGAN00001249171,EGAN00001249172,EGAN00001249173,EGAN00001249174,EGAN00001249175,EGAN00001249176,EGAN00001249177,EGAN00001249178,EGAN00001249179,EGAN00001249180,EGAN00001249181,EGAN00001249182,EGAN00001249183,EGAN00001249184,EGAN00001249185,EGAN00001249186,EGAN00001249187,EGAN00001249188,EGAN00001249189,EGAN00001249190,EGAN00001249191,EGAN00001249192,EGAN00001249193,EGAN00001249194,EGAN00001249195,EGAN00001249196,EGAN00001249197,EGAN00001249198,EGAN00001249199,EGAN00001249200,EGAN00001249201,EGAN00001249202,EGAN00001249203,EGAN00001249204,EGAN00001249205,EGAN00001249206,EGAN00001249207,EGAN00001249208,EGAN00001249209,EGAN00001249210,EGAN00001249211,EGAN00001249212,EGAN00001249213,EGAN00001249214,EGAN00001249215,EGAN00001249216,EGAN00001249217,EGAN00001249218,EGAN00001249219,EGAN00001249220,EGAN00001249221,EGAN00001249222,EGAN00001249223,EGAN00001249224,EGAN00001249225,EGAN00001249226,EGAN00001249227,EGAN00001249228,EGAN00001249229,EGAN00001249230,EGAN00001249231,EGAN00001249232,EGAN00001249233,EGAN00001249234,EGAN00001249235,EGAN00001249236,EGAN00001249237,EGAN00001249238,EGAN00001249239,EGAN00001249240,EGAN00001249241,EGAN00001249242,EGAN00001249243,EGAN00001249244,EGAN00001249245,EGAN00001249246,EGAN00001249247,EGAN00001249248,EGAN00001249249,EGAN00001249250,EGAN00001249251,EGAN00001249252,EGAN00001249253,EGAN00001249254,EGAN00001249255,EGAN00001249256,EGAN00001249257,EGAN00001249258,EGAN00001249259,EGAN00001249260,EGAN00001249261,EGAN00001249262,EGAN00001249263,EGAN00001249264,EGAN00001249265,EGAN00001249266,EGAN00001249267,EGAN00001249268,EGAN00001249269,EGAN00001249270,EGAN00001249271,EGAN00001249272,EGAN00001249273,EGAN00001249274,EGAN00001249275,EGAN00001249276,EGAN00001249277,EGAN00001249278,EGAN00001249279,EGAN00001249280,EGAN00001249281,EGAN00001249282,EGAN00001249283,EGAN00001249284,EGAN00001249285,EGAN00001249286,EGAN00001249287,EGAN00001249288,EGAN00001249289,EGAN00001249290,EGAN00001249291,EGAN00001249292,EGAN00001249293,EGAN00001249294,EGAN00001249295,EGAN00001249296,EGAN00001249297,EGAN00001249298,EGAN00001249299,EGAN00001249300,EGAN00001249301,EGAN00001249302,EGAN00001249303,EGAN00001249304,EGAN00001249305,EGAN00001249306,EGAN00001249307,EGAN00001249308,EGAN00001249309,EGAN00001249310,EGAN00001249311,EGAN00001249312,EGAN00001249313,EGAN00001249314,EGAN00001249315,EGAN00001249316,EGAN00001249317,EGAN00001249318,EGAN00001249319,EGAN00001249320,EGAN00001249321,EGAN00001249322,EGAN00001249323,EGAN00001249324,EGAN00001249325,EGAN00001249326,EGAN00001249327,EGAN00001249328,EGAN00001249329,EGAN00001249330,EGAN00001249331,EGAN00001249332,EGAN00001249333,EGAN00001249334,EGAN00001249335,EGAN00001249336,EGAN00001249337,EGAN00001249338,EGAN00001249339,EGAN00001249340,EGAN00001249341,EGAN00001249342,EGAN00001249343,EGAN00001249344,EGAN00001249345,EGAN00001249346,EGAN00001249347,EGAN00001249348,EGAN00001249349,EGAN00001249350,EGAN00001249351,EGAN00001249352,EGAN00001249353,EGAN00001249354,EGAN00001249355,EGAN00001249356,EGAN00001249357,EGAN00001249358,EGAN00001249359,EGAN00001249360,EGAN00001249361,EGAN00001249362,EGAN00001249363,EGAN00001249364,EGAN00001249365,EGAN00001249366,EGAN00001249367,EGAN00001249368,EGAN00001249369,EGAN00001249370,EGAN00001249371,EGAN00001249372,EGAN00001249373,EGAN00001249374,EGAN00001249375,EGAN00001249376,EGAN00001249377,EGAN00001249378,EGAN00001249379,EGAN00001249380,EGAN00001249381,EGAN00001249382,EGAN00001249383,EGAN00001249384,EGAN00001249385,EGAN00001249386,EGAN00001249387,EGAN00001249388,EGAN00001249389,EGAN00001249390,EGAN00001249391,EGAN00001249392,EGAN00001249393,EGAN00001249394,EGAN00001249395,EGAN00001249396,EGAN00001249397,EGAN00001249398,EGAN00001249399,EGAN00001249400,EGAN00001249401,EGAN00001249402,EGAN00001249403,EGAN00001249404,EGAN00001249405,EGAN00001249406,EGAN00001249407,EGAN00001249408,EGAN00001249409,EGAN00001249410,EGAN00001249411,EGAN00001249412,EGAN00001249413,EGAN00001249414,EGAN00001249415,EGAN00001249416,EGAN00001249417,EGAN00001249418,EGAN00001249419,EGAN00001249420,EGAN00001249421,EGAN00001249422,EGAN00001249423,EGAN00001249424,EGAN00001249425,EGAN00001249426,EGAN00001249427,EGAN00001249428,EGAN00001249429,EGAN00001249430,EGAN00001249431,EGAN00001249432,EGAN00001249433,EGAN00001249434,EGAN00001249435,EGAN00001249436,EGAN00001249437,EGAN00001249438,EGAN00001249439,EGAN00001249440,EGAN00001249441,EGAN00001249442,EGAN00001249443,EGAN00001249444,EGAN00001249445,EGAN00001249446,EGAN00001249447,EGAN00001249448,EGAN00001249449,EGAN00001249450,EGAN00001249451,EGAN00001249452,EGAN00001249453,EGAN00001249454,EGAN00001249455,EGAN00001249456,EGAN00001249457,EGAN00001249458,EGAN00001249459,EGAN00001249460,EGAN00001249461,EGAN00001249462,EGAN00001249463,EGAN00001249464,EGAN00001249465,EGAN00001249466,EGAN00001249467,EGAN00001249468,EGAN00001249469 STUDY_NAME=EGAS00001000814: The aim of this study is to ascertain whether leukaemic mutations exist within the blood of people with otherwise normal haematopoeisis. To satisfy this aim we plan to look for 7 known leukaemic mutations in the whole blood DNA of a large cohort of blood donors who have normal haematopoesis. Genomic regions around mutational sites have been amplified using a 2 step PCR process which involves barcoding of individual patients PLATFORM_UNIT=141124_MS3_14786_A_MS2775046-500V2_1 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 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:0.0.180 CL:bamadapterfind level=0 @PG ID:BamIndexDecoder PN:BamIndexDecoder PP:bamadapterfind DS:A command-line tool to decode multiplexed bam file VN:V1.16 CL:uk.ac.sanger.npg.picard.BamIndexDecoder INPUT=/dev/stdin OUTPUT=/dev/stdout BARCODE_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/metadata_cache_14786/lane_1.taglist METRICS_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/14786_1.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:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamIndexDecoder 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:V1.16 CL:uk.ac.sanger.npg.picard.SplitBamByReadGroup INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/14786_1.bam OUTPUT_PREFIX=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/lane1/14786_1 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:bwa_aln PN:bwa PP:SplitBamByReadGroup VN:0.5.10-tpx CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa aln -q 15 -t 12 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta -b1 /nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/lane1/14786_1#71.bam > /tmp/xtxVbXfkC9/1.sai @PG ID:bwa_aln_1 PN:bwa PP:bwa_aln VN:0.5.10-tpx CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa aln -q 15 -t 12 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta -b2 /nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/lane1/14786_1#71.bam > /tmp/xtxVbXfkC9/2.sai @PG ID:bwa_sam PN:bwa PP:bwa_aln_1 VN:0.5.10-tpx CL:/software/solexa/pkg/bwa/bwa-0.5.10-mt_fixes/bwa sampe -t 6 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta /tmp/xtxVbXfkC9/1.sai /tmp/xtxVbXfkC9/2.sai /nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/lane1/14786_1#71.bam /nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/lane1/14786_1#71.bam @PG ID:Picard_SamFormatConverter PN:SamFormatConverter PP:bwa_sam VN:1.72(1230) CL:/software/jdk1.7.0_25/bin/java -Xmx1000m -jar /software/solexa/pkg/picard/picard-tools-1.72/SamFormatConverter.jar VALIDATION_STRINGENCY=SILENT INPUT=/dev/stdin OUTPUT=/dev/stdout COMPRESSION_LEVEL=0 @PG ID:samtools_fixmate PN:samtools PP:Picard_SamFormatConverter VN:0.1.18 (r982:295) CL:/software/solexa/pkg/samtools/samtools-0.1.18/samtools fixmate - - @PG ID:BamMerger PN:BamMerger PP:samtools_fixmate 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:V1.16 CL:uk.ac.sanger.npg.picard.BamMerger ALIGNED_BAM=/dev/stdin ALIGNMENT_PROGRAM_ID=NULL KEEP_ALL_PG=true INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/lane1/14786_1#71.bam OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/archive/lane1/14786_1#71.bam KEEP_EXTRA_UNMAPPED_READS=true VALIDATION_STRINGENCY=SILENT CREATE_MD5_FILE=true REPLACE_ALIGNED_BASE_QUALITY=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false @PG ID:bamsort PN:bamsort PP:BamMerger VN:0.0.180 CL:/software/hpag/biobambam/0.0.180/bin/bamsort tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/archive/lane1/gudKo70DTR/ @PG ID:bammarkduplicates2 PN:bammarkduplicates2 PP:bamsort VN:0.0.180 CL:/software/hpag/biobambam/0.0.180/bin/bammarkduplicates2 I=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/archive/lane1/gudKo70DTR/sorted.bam O=/dev/stdout tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/archive/lane1/gudKo70DTR/ M=/tmp/aYyI6txLbU level=0 @PG ID:BamTagStripper PN:BamTagStripper PP:bammarkduplicates2 DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.16 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/dev/stdout TAG_TO_KEEP=[a3, aa, af, ah, as, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS3_14786_A_MS2775046-500V2/Data/Intensities/BAM_basecalls_20141126-014433/no_cal/archive/lane1/gudKo70DTR] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=false CREATE_MD5_FILE=false QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 @PG ID:scramble PN:scramble PP:BamTagStripper VN:1.13.7 CL:/software/badger/bin/scramble -I bam -O cram -r /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta @SQ SN:1 LN:249250621 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Human @SQ SN:2 LN:243199373 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:a0d9851da00400dec1098a9255ac712e SP:Human @SQ SN:3 LN:198022430 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Human @SQ SN:4 LN:191154276 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:23dccd106897542ad87d2765d28a19a1 SP:Human @SQ SN:5 LN:180915260 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:0740173db9ffd264d728f32784845cd7 SP:Human @SQ SN:6 LN:171115067 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1d3a93a248d92a729ee764823acbbc6b SP:Human @SQ SN:7 LN:159138663 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:618366e953d6aaad97dbe4777c29375e SP:Human @SQ SN:8 LN:146364022 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:96f514a9929e410c6651697bded59aec SP:Human @SQ SN:9 LN:141213431 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:3e273117f15e0a400f01055d9f393768 SP:Human @SQ SN:10 LN:135534747 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:988c28e000e84c26d552359af1ea2e1d SP:Human @SQ SN:11 LN:135006516 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Human @SQ SN:12 LN:133851895 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:51851ac0e1a115847ad36449b0015864 SP:Human @SQ SN:13 LN:115169878 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:283f8d7892baa81b510a015719ca7b0b SP:Human @SQ SN:14 LN:107349540 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:98f3cae32b2a2e9524bc19813927542e SP:Human @SQ SN:15 LN:102531392 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:e5645a794a8238215b2cd77acb95a078 SP:Human @SQ SN:16 LN:90354753 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Human @SQ SN:17 LN:81195210 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Human @SQ SN:18 LN:78077248 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Human @SQ SN:19 LN:59128983 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1aacd71f30db8e561810913e0b72636d SP:Human @SQ SN:20 LN:63025520 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Human @SQ SN:21 LN:48129895 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:2979a6085bfe28e3ad6f552f361ed74d SP:Human @SQ SN:22 LN:51304566 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:a718acaa6135fdca8357d5bfe94211dd SP:Human @SQ SN:X LN:155270560 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Human @SQ SN:Y LN:59373566 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Human @SQ SN:MT LN:16569 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:c68f52674c9fb33aef52dcf399755519 SP:Human @SQ SN:GL000207.1 LN:4262 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Human @SQ SN:GL000226.1 LN:15008 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Human @SQ SN:GL000229.1 LN:19913 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Human @SQ SN:GL000231.1 LN:27386 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Human @SQ SN:GL000210.1 LN:27682 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:851106a74238044126131ce2a8e5847c SP:Human @SQ SN:GL000239.1 LN:33824 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:99795f15702caec4fa1c4e15f8a29c07 SP:Human @SQ SN:GL000235.1 LN:34474 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Human @SQ SN:GL000201.1 LN:36148 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Human @SQ SN:GL000247.1 LN:36422 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:7de00226bb7df1c57276ca6baabafd15 SP:Human @SQ SN:GL000245.1 LN:36651 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:89bc61960f37d94abf0df2d481ada0ec SP:Human @SQ SN:GL000197.1 LN:37175 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Human @SQ SN:GL000203.1 LN:37498 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:96358c325fe0e70bee73436e8bb14dbd SP:Human @SQ SN:GL000246.1 LN:38154 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Human @SQ SN:GL000249.1 LN:38502 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1d78abec37c15fe29a275eb08d5af236 SP:Human @SQ SN:GL000196.1 LN:38914 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Human @SQ SN:GL000248.1 LN:39786 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:5a8e43bec9be36c7b49c84d585107776 SP:Human @SQ SN:GL000244.1 LN:39929 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:0996b4475f353ca98bacb756ac479140 SP:Human @SQ SN:GL000238.1 LN:39939 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:131b1efc3270cc838686b54e7c34b17b SP:Human @SQ SN:GL000202.1 LN:40103 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:06cbf126247d89664a4faebad130fe9c SP:Human @SQ SN:GL000234.1 LN:40531 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:93f998536b61a56fd0ff47322a911d4b SP:Human @SQ SN:GL000232.1 LN:40652 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:3e06b6741061ad93a8587531307057d8 SP:Human @SQ SN:GL000206.1 LN:41001 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Human @SQ SN:GL000240.1 LN:41933 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Human @SQ SN:GL000236.1 LN:41934 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Human @SQ SN:GL000241.1 LN:42152 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Human @SQ SN:GL000243.1 LN:43341 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:cc34279a7e353136741c9fce79bc4396 SP:Human @SQ SN:GL000242.1 LN:43523 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Human @SQ SN:GL000230.1 LN:43691 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:b4eb71ee878d3706246b7c1dbef69299 SP:Human @SQ SN:GL000237.1 LN:45867 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Human @SQ SN:GL000233.1 LN:45941 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:7fed60298a8d62ff808b74b6ce820001 SP:Human @SQ SN:GL000204.1 LN:81310 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:efc49c871536fa8d79cb0a06fa739722 SP:Human @SQ SN:GL000198.1 LN:90085 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:868e7784040da90d900d2d1b667a1383 SP:Human @SQ SN:GL000208.1 LN:92689 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Human @SQ SN:GL000191.1 LN:106433 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Human @SQ SN:GL000227.1 LN:128374 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:a4aead23f8053f2655e468bcc6ecdceb SP:Human @SQ SN:GL000228.1 LN:129120 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Human @SQ SN:GL000214.1 LN:137718 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:46c2032c37f2ed899eb41c0473319a69 SP:Human @SQ SN:GL000221.1 LN:155397 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:3238fb74ea87ae857f9c7508d315babb SP:Human @SQ SN:GL000209.1 LN:159169 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Human @SQ SN:GL000218.1 LN:161147 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Human @SQ SN:GL000220.1 LN:161802 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:fc35de963c57bf7648429e6454f1c9db SP:Human @SQ SN:GL000213.1 LN:164239 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:9d424fdcc98866650b58f004080a992a SP:Human @SQ SN:GL000211.1 LN:166566 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Human @SQ SN:GL000199.1 LN:169874 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:569af3b73522fab4b40995ae4944e78e SP:Human @SQ SN:GL000217.1 LN:172149 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Human @SQ SN:GL000216.1 LN:172294 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:642a232d91c486ac339263820aef7fe0 SP:Human @SQ SN:GL000215.1 LN:172545 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:5eb3b418480ae67a997957c909375a73 SP:Human @SQ SN:GL000205.1 LN:174588 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Human @SQ SN:GL000219.1 LN:179198 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Human @SQ SN:GL000224.1 LN:179693 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Human @SQ SN:GL000223.1 LN:180455 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Human @SQ SN:GL000195.1 LN:182896 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:5d9ec007868d517e73543b005ba48535 SP:Human @SQ SN:GL000212.1 LN:186858 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:563531689f3dbd691331fd6c5730a88b SP:Human @SQ SN:GL000222.1 LN:186861 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Human @SQ SN:GL000200.1 LN:187035 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Human @SQ SN:GL000193.1 LN:189789 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Human @SQ SN:GL000194.1 LN:191469 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Human @SQ SN:GL000225.1 LN:211173 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:63945c3e6962f28ffd469719a747e73c SP:Human @SQ SN:GL000192.1 LN:547496 UR:/lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta AS:NCBI37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Human