@HD VN:1.4 SO:coordinate @RG ID:1#46 PL:ILLUMINA PU:141124_MS5_14783_A_MS2780791-500V2_1#46 LB:12396318 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:EGAN00001248747 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_MS5_14783_A_MS2780791-500V2/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS5_14783_A_MS2780791-500V2/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=EGAN00001248702,EGAN00001248703,EGAN00001248704,EGAN00001248705,EGAN00001248706,EGAN00001248707,EGAN00001248708,EGAN00001248709,EGAN00001248710,EGAN00001248711,EGAN00001248712,EGAN00001248713,EGAN00001248714,EGAN00001248715,EGAN00001248716,EGAN00001248717,EGAN00001248718,EGAN00001248719,EGAN00001248720,EGAN00001248721,EGAN00001248722,EGAN00001248723,EGAN00001248724,EGAN00001248725,EGAN00001248726,EGAN00001248727,EGAN00001248728,EGAN00001248729,EGAN00001248730,EGAN00001248731,EGAN00001248732,EGAN00001248733,EGAN00001248734,EGAN00001248735,EGAN00001248736,EGAN00001248737,EGAN00001248738,EGAN00001248739,EGAN00001248740,EGAN00001248741,EGAN00001248742,EGAN00001248743,EGAN00001248744,EGAN00001248745,EGAN00001248746,EGAN00001248747,EGAN00001248748,EGAN00001248749,EGAN00001248750,EGAN00001248751,EGAN00001248752,EGAN00001248753,EGAN00001248754,EGAN00001248755,EGAN00001248756,EGAN00001248757,EGAN00001248758,EGAN00001248759,EGAN00001248760,EGAN00001248761,EGAN00001248762,EGAN00001248763,EGAN00001248764,EGAN00001248765,EGAN00001248766,EGAN00001248767,EGAN00001248768,EGAN00001248769,EGAN00001248770,EGAN00001248771,EGAN00001248772,EGAN00001248773,EGAN00001248774,EGAN00001248775,EGAN00001248776,EGAN00001248777,EGAN00001248778,EGAN00001248779,EGAN00001248780,EGAN00001248781,EGAN00001248782,EGAN00001248783,EGAN00001248784,EGAN00001248785,EGAN00001248786,EGAN00001248787,EGAN00001248788,EGAN00001248789,EGAN00001248790,EGAN00001248791,EGAN00001248792,EGAN00001248793,EGAN00001248794,EGAN00001248795,EGAN00001248796,EGAN00001248797,EGAN00001248798,EGAN00001248799,EGAN00001248800,EGAN00001248801,EGAN00001248802,EGAN00001248803,EGAN00001248804,EGAN00001248805,EGAN00001248806,EGAN00001248807,EGAN00001248808,EGAN00001248809,EGAN00001248810,EGAN00001248811,EGAN00001248812,EGAN00001248813,EGAN00001248814,EGAN00001248815,EGAN00001248816,EGAN00001248817,EGAN00001248818,EGAN00001248819,EGAN00001248820,EGAN00001248821,EGAN00001248822,EGAN00001248823,EGAN00001248824,EGAN00001248825,EGAN00001248826,EGAN00001248827,EGAN00001248828,EGAN00001248829,EGAN00001248830,EGAN00001248831,EGAN00001248832,EGAN00001248833,EGAN00001248834,EGAN00001248835,EGAN00001248836,EGAN00001248837,EGAN00001248838,EGAN00001248839,EGAN00001248840,EGAN00001248841,EGAN00001248842,EGAN00001248843,EGAN00001248844,EGAN00001248845,EGAN00001248846,EGAN00001248847,EGAN00001248848,EGAN00001248849,EGAN00001248850,EGAN00001248851,EGAN00001248852,EGAN00001248853,EGAN00001248854,EGAN00001248855,EGAN00001248856,EGAN00001248857,EGAN00001248858,EGAN00001248859,EGAN00001248860,EGAN00001248861,EGAN00001248862,EGAN00001248863,EGAN00001248864,EGAN00001248865,EGAN00001248866,EGAN00001248867,EGAN00001248868,EGAN00001248869,EGAN00001248870,EGAN00001248871,EGAN00001248872,EGAN00001248873,EGAN00001248874,EGAN00001248875,EGAN00001248876,EGAN00001248877,EGAN00001248878,EGAN00001248879,EGAN00001248880,EGAN00001248881,EGAN00001248882,EGAN00001248883,EGAN00001248884,EGAN00001248885,EGAN00001248886,EGAN00001248887,EGAN00001248888,EGAN00001248889,EGAN00001248890,EGAN00001248891,EGAN00001248892,EGAN00001248893,EGAN00001248894,EGAN00001248895,EGAN00001248896,EGAN00001248897,EGAN00001248898,EGAN00001248899,EGAN00001248900,EGAN00001248901,EGAN00001248902,EGAN00001248903,EGAN00001248904,EGAN00001248905,EGAN00001248906,EGAN00001248907,EGAN00001248908,EGAN00001248909,EGAN00001248910,EGAN00001248911,EGAN00001248912,EGAN00001248913,EGAN00001248914,EGAN00001248915,EGAN00001248916,EGAN00001248917,EGAN00001248918,EGAN00001248919,EGAN00001248920,EGAN00001248921,EGAN00001248922,EGAN00001248923,EGAN00001248924,EGAN00001248925,EGAN00001248926,EGAN00001248927,EGAN00001248928,EGAN00001248929,EGAN00001248930,EGAN00001248931,EGAN00001248932,EGAN00001248933,EGAN00001248934,EGAN00001248935,EGAN00001248936,EGAN00001248937,EGAN00001248938,EGAN00001248939,EGAN00001248940,EGAN00001248941,EGAN00001248942,EGAN00001248943,EGAN00001248944,EGAN00001248945,EGAN00001248946,EGAN00001248947,EGAN00001248948,EGAN00001248949,EGAN00001248950,EGAN00001248951,EGAN00001248952,EGAN00001248953,EGAN00001248954,EGAN00001248955,EGAN00001248956,EGAN00001248957,EGAN00001248958,EGAN00001248959,EGAN00001248960,EGAN00001248961,EGAN00001248962,EGAN00001248963,EGAN00001248964,EGAN00001248965,EGAN00001248966,EGAN00001248967,EGAN00001248968,EGAN00001248969,EGAN00001248970,EGAN00001248971,EGAN00001248972,EGAN00001248973,EGAN00001248974,EGAN00001248975,EGAN00001248976,EGAN00001248977,EGAN00001248978,EGAN00001248979,EGAN00001248980,EGAN00001248981,EGAN00001248982,EGAN00001248983,EGAN00001248984,EGAN00001248985,EGAN00001248986,EGAN00001248987,EGAN00001248988,EGAN00001248989,EGAN00001248990,EGAN00001248991,EGAN00001248992,EGAN00001248993,EGAN00001248994,EGAN00001248995,EGAN00001248996,EGAN00001248997,EGAN00001248998,EGAN00001248999,EGAN00001249000,EGAN00001249001,EGAN00001249002,EGAN00001249003,EGAN00001249004,EGAN00001249005,EGAN00001249006,EGAN00001249007,EGAN00001249008,EGAN00001249009,EGAN00001249010,EGAN00001249011,EGAN00001249012,EGAN00001249013,EGAN00001249014,EGAN00001249015,EGAN00001249016,EGAN00001249017,EGAN00001249018,EGAN00001249019,EGAN00001249020,EGAN00001249021,EGAN00001249022,EGAN00001249023,EGAN00001249024,EGAN00001249025,EGAN00001249026,EGAN00001249027,EGAN00001249028,EGAN00001249029,EGAN00001249030,EGAN00001249031,EGAN00001249032,EGAN00001249033,EGAN00001249034,EGAN00001249035,EGAN00001249036,EGAN00001249037,EGAN00001249038,EGAN00001249039,EGAN00001249040,EGAN00001249041,EGAN00001249042,EGAN00001249043,EGAN00001249044,EGAN00001249045,EGAN00001249046,EGAN00001249047,EGAN00001249048,EGAN00001249049,EGAN00001249050,EGAN00001249051,EGAN00001249052,EGAN00001249053,EGAN00001249054,EGAN00001249055,EGAN00001249056,EGAN00001249057,EGAN00001249058,EGAN00001249059,EGAN00001249060,EGAN00001249061,EGAN00001249062,EGAN00001249063,EGAN00001249064,EGAN00001249065,EGAN00001249066,EGAN00001249067,EGAN00001249068,EGAN00001249069,EGAN00001249070,EGAN00001249071,EGAN00001249072,EGAN00001249073,EGAN00001249074,EGAN00001249075,EGAN00001249076,EGAN00001249077,EGAN00001249078,EGAN00001249079,EGAN00001249080,EGAN00001249081,EGAN00001249082,EGAN00001249083,EGAN00001249084,EGAN00001249085 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_MS5_14783_A_MS2780791-500V2_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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/metadata_cache_14783/lane_1.taglist METRICS_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/14783_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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/14783_1.bam OUTPUT_PREFIX=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/lane1/14783_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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/lane1/14783_1#46.bam > /tmp/s494_K1N20/1.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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/lane1/14783_1#46.bam > /tmp/s494_K1N20/2.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/s494_K1N20/1.sai /tmp/s494_K1N20/2.sai /nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/lane1/14783_1#46.bam /nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/lane1/14783_1#46.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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/lane1/14783_1#46.bam OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/archive/lane1/14783_1#46.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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/archive/lane1/NWx_Dth66Y/ @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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/archive/lane1/NWx_Dth66Y/sorted.bam O=/dev/stdout tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/141124_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/archive/lane1/NWx_Dth66Y/ M=/tmp/KmHuEjPoi8 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_MS5_14783_A_MS2780791-500V2/Data/Intensities/BAM_basecalls_20141126-015503/no_cal/archive/lane1/NWx_Dth66Y] 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