@HD VN:1.4 SO:coordinate @RG ID:1#13 PL:ILLUMINA PU:141216_MS7_14996_A_MS2786383-500V2_1#13 LB:12543893 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:2014-12-16T00:00:00+0000 SM:UKHLS_1165 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/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=UKHLS_1153,UKHLS_1154,UKHLS_1155,UKHLS_1156,UKHLS_1157,UKHLS_1158,UKHLS_1159,UKHLS_1160,UKHLS_1161,UKHLS_1162,UKHLS_1163,UKHLS_1164,UKHLS_1165,UKHLS_1166,UKHLS_1167,UKHLS_1168,UKHLS_1169,UKHLS_1170,UKHLS_1171,UKHLS_1172,UKHLS_1173,UKHLS_1174,UKHLS_1175,UKHLS_1176,UKHLS_1177,UKHLS_1178,UKHLS_1179,UKHLS_1180,UKHLS_1181,UKHLS_1182,UKHLS_1183,UKHLS_1184,UKHLS_1185,UKHLS_1186,UKHLS_1187,UKHLS_1188,UKHLS_1189,UKHLS_1190,UKHLS_1191,UKHLS_1192,UKHLS_1193,UKHLS_1194,UKHLS_1195,UKHLS_1196,UKHLS_1197,UKHLS_1198,UKHLS_1199,UKHLS_1200,UKHLS_1201,UKHLS_1202,UKHLS_1203,UKHLS_1204,UKHLS_1205,UKHLS_1206,UKHLS_1207,UKHLS_1208,UKHLS_1209,UKHLS_1210,UKHLS_1211,UKHLS_1212,UKHLS_1213,UKHLS_1214,UKHLS_1215,UKHLS_1216,UKHLS_1217,UKHLS_1218,UKHLS_1219,UKHLS_1220,UKHLS_1221,UKHLS_1222,UKHLS_1223,UKHLS_1224,UKHLS_1225,UKHLS_1226,UKHLS_1227,UKHLS_1228,UKHLS_1229,UKHLS_1230,UKHLS_1231,UKHLS_1232,UKHLS_1233,UKHLS_1234,UKHLS_1235,UKHLS_1236,UKHLS_1237,UKHLS_1238,UKHLS_1239,UKHLS_1240,UKHLS_1241,UKHLS_1242,UKHLS_1243,UKHLS_1244,UKHLS_1245,UKHLS_1246,UKHLS_1247,UKHLS_1248,UKHLS_1249,UKHLS_1250,UKHLS_1251,UKHLS_1252,UKHLS_1253,UKHLS_1254,UKHLS_1255,UKHLS_1256,UKHLS_1257,UKHLS_1258,UKHLS_1259,UKHLS_1260,UKHLS_1261,UKHLS_1262,UKHLS_1263,UKHLS_1264,UKHLS_1265,UKHLS_1266,UKHLS_1267,UKHLS_1268,UKHLS_1269,UKHLS_1270,UKHLS_1271,UKHLS_1272,UKHLS_1273,UKHLS_1274,UKHLS_1275,UKHLS_1276,UKHLS_1277,UKHLS_1278,UKHLS_1279,UKHLS_1280,UKHLS_1281,UKHLS_1282,UKHLS_1283,UKHLS_1284,UKHLS_1285,UKHLS_1286,UKHLS_1287,UKHLS_1288,UKHLS_1289,UKHLS_1290,UKHLS_1291,UKHLS_1292,UKHLS_1293,UKHLS_1294,UKHLS_1295,UKHLS_1296,UKHLS_1297,UKHLS_1298,UKHLS_1299,UKHLS_1300,UKHLS_1301,UKHLS_1302,UKHLS_1303,UKHLS_1304,UKHLS_1305,UKHLS_1306,UKHLS_1307,UKHLS_1308,UKHLS_1309,UKHLS_1310,UKHLS_1311,UKHLS_1312,UKHLS_1313,UKHLS_1314,UKHLS_1315,UKHLS_1316,UKHLS_1317,UKHLS_1318,UKHLS_1319,UKHLS_1320,UKHLS_1321,UKHLS_1322,UKHLS_1323,UKHLS_1324,UKHLS_1325,UKHLS_1326,UKHLS_1327,UKHLS_1328,UKHLS_1329,UKHLS_1330,UKHLS_1331,UKHLS_1332,UKHLS_1333,UKHLS_1334,UKHLS_1335,UKHLS_1336,UKHLS_1337,UKHLS_1338,UKHLS_1339,UKHLS_1340,UKHLS_1341,UKHLS_1342,UKHLS_1343,UKHLS_1344,UKHLS_1345,UKHLS_1346,UKHLS_1347,UKHLS_1348,UKHLS_1349,UKHLS_1350,UKHLS_1351,UKHLS_1352,UKHLS_1353,UKHLS_1354,UKHLS_1355,UKHLS_1356,UKHLS_1357,UKHLS_1358,UKHLS_1359,UKHLS_1360,UKHLS_1361,UKHLS_1362,UKHLS_1363,UKHLS_1364,UKHLS_1365,UKHLS_1366,UKHLS_1367,UKHLS_1368,UKHLS_1369,UKHLS_1370,UKHLS_1371,UKHLS_1372,UKHLS_1373,UKHLS_1374,UKHLS_1375,UKHLS_1376,UKHLS_1377,UKHLS_1378,UKHLS_1379,UKHLS_1380,UKHLS_1381,UKHLS_1382,UKHLS_1383,UKHLS_1384,UKHLS_1385,UKHLS_1386,UKHLS_1387,UKHLS_1388,UKHLS_1389,UKHLS_1390,UKHLS_1391,UKHLS_1392,UKHLS_1393,UKHLS_1394,UKHLS_1395,UKHLS_1396,UKHLS_1397,UKHLS_1398,UKHLS_1399,UKHLS_1400,UKHLS_1401,UKHLS_1402,UKHLS_1403,UKHLS_1404,UKHLS_1405,UKHLS_1406,UKHLS_1407,UKHLS_1408,UKHLS_1409,UKHLS_1410,UKHLS_1411,UKHLS_1412,UKHLS_1413,UKHLS_1414,UKHLS_1415,UKHLS_1416,UKHLS_1417,UKHLS_1418,UKHLS_1419,UKHLS_1420,UKHLS_1421,UKHLS_1422,UKHLS_1423,UKHLS_1424,UKHLS_1425,UKHLS_1426,UKHLS_1427,UKHLS_1428,UKHLS_1429,UKHLS_1430,UKHLS_1431,UKHLS_1432,UKHLS_1433,UKHLS_1434,UKHLS_1435,UKHLS_1436,UKHLS_1437,UKHLS_1438,UKHLS_1439,UKHLS_1440,UKHLS_1441,UKHLS_1442,UKHLS_1443,UKHLS_1444,UKHLS_1445,UKHLS_1446,UKHLS_1447,UKHLS_1448,UKHLS_1449,UKHLS_1450,UKHLS_1451,UKHLS_1452,UKHLS_1453,UKHLS_1454,UKHLS_1455,UKHLS_1456,UKHLS_1457,UKHLS_1458,UKHLS_1459,UKHLS_1460,UKHLS_1461,UKHLS_1462,UKHLS_1463,UKHLS_1464,UKHLS_1465,UKHLS_1466,UKHLS_1467,UKHLS_1468,UKHLS_1469,UKHLS_1470,UKHLS_1471,UKHLS_1472,UKHLS_1473,UKHLS_1474,UKHLS_1475,UKHLS_1476,UKHLS_1477,UKHLS_1478,UKHLS_1479,UKHLS_1480,UKHLS_1481,UKHLS_1482,UKHLS_1483,UKHLS_1484,UKHLS_1485,UKHLS_1486,UKHLS_1487,UKHLS_1488,UKHLS_1489,UKHLS_1490,UKHLS_1491,UKHLS_1492,UKHLS_1493,UKHLS_1494,UKHLS_1495,UKHLS_1496,UKHLS_1497,UKHLS_1498,UKHLS_1499,UKHLS_1500,UKHLS_1501,UKHLS_1502,UKHLS_1503,UKHLS_1504,UKHLS_1505,UKHLS_1506,UKHLS_1507,UKHLS_1508,UKHLS_1509,UKHLS_1510,UKHLS_1511,UKHLS_1512,UKHLS_1513,UKHLS_1514,UKHLS_1515,UKHLS_1516,UKHLS_1517,UKHLS_1518,UKHLS_1519,UKHLS_1520,UKHLS_1521,UKHLS_1522,UKHLS_1523,UKHLS_1524,UKHLS_1525,UKHLS_1526,UKHLS_1527,UKHLS_1528,UKHLS_1529,UKHLS_1530,UKHLS_1531,UKHLS_1532,UKHLS_1533,UKHLS_1534,UKHLS_1535,UKHLS_1536 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=141216_MS7_14996_A_MS2786383-500V2_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/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/metadata_cache_14996/lane_1.taglist METRICS_FILE=/nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/14996_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/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/14996_1.bam OUTPUT_PREFIX=/nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/lane1/14996_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 14 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta -b1 /nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/lane1/14996_1#13.bam > /tmp/Df64TmN7un/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 14 /lustre/scratch110/srpipe/references/Homo_sapiens/1000Genomes/all/bwa/human_g1k_v37.fasta -b2 /nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/lane1/14996_1#13.bam > /tmp/Df64TmN7un/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/Df64TmN7un/1.sai /tmp/Df64TmN7un/2.sai /nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/lane1/14996_1#13.bam /nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/lane1/14996_1#13.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/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/lane1/14996_1#13.bam OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/archive/lane1/14996_1#13.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/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/archive/lane1/Z8gHLce0HY/ @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/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/archive/lane1/Z8gHLce0HY/sorted.bam O=/dev/stdout tmpfile=/nfs/sf49/ILorHSorMS_sf49/analysis/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/archive/lane1/Z8gHLce0HY/ M=/tmp/po_Uu5KMHV 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/141216_MS7_14996_A_MS2786383-500V2/Data/Intensities/BAM_basecalls_20141218-015226/no_cal/archive/lane1/Z8gHLce0HY] 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