基因数据处理34之使用samtools和bcftools进行变异分析
发布时间：2021-03-07 06:29:56 所属栏目：大数据 来源：网络整理
导读：1.指令： （1） samtools mpileup -vf Homo_sapiens_assembly19chr20 .fasta NA12878_snp_A2G_chr20_225058 .sorted .bam NA12878_snp_A2G_chr20_225058 .variants 或者： samtools mpileup -vf Homo_sapiens_assembly19chr20 .fasta NA12878_snp_A2G_chr20_
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1.指令： samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam > NA12878_snp_A2G_chr20_225058.variants 或者： samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam > NA12878_snp_A2G_chr20_225058.vcf （2） bcftools call -mv NA12878_snp_A2G_chr20_225058.vcf >NA12878_snp_A2G_chr20_225058.raw.vcf （3） bcftools filter -s LowQual -e '%QUAL<20 || DP>100' NA12878_snp_A2G_chr20_225058.raw.vcf > NA12878_snp_A2G_chr20_225058.flt.vcf bcftools view 可以查看bcf数据结果。
xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ cat NA12878_snp_A2G_chr20_225058.flt.vcf ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##samtoolsVersion=1.3.1-24-gf458b7c+htslib-1.3.1-35-g481752c ##samtoolsCommand=samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam ##reference=file://Homo_sapiens_assembly19chr20.fasta ##contig=<ID=20,length=63025520> ##ALT=<ID=*,Description="Represents allele(s) other than observed."> ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> ##INFO=<ID=IMF,Type=Float,Description="Maximum fraction of reads supporting an indel"> ##INFO=<ID=DP,Description="Raw read depth"> ##INFO=<ID=VDB,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> ##INFO=<ID=RPB,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> ##INFO=<ID=MQB,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> ##INFO=<ID=BQB,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> ##INFO=<ID=MQSB,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> ##INFO=<ID=SGB,Description="Segregation based metric."> ##INFO=<ID=MQ0F,Description="Fraction of MQ0 reads (smaller is better)"> ##FORMAT=<ID=PL,Number=G,Description="List of Phred-scaled genotype likelihoods"> ##FORMAT=<ID=GT,Type=String,Description="Genotype"> ##INFO=<ID=ICB,Description="Inbreeding Coefficient Binomial test (bigger is better)"> ##INFO=<ID=HOB,Description="Bias in the number of HOMs number (smaller is better)"> ##INFO=<ID=AC,Number=A,Description="Allele count in genotypes for each ALT allele,in the same order as listed"> ##INFO=<ID=AN,Description="Total number of alleles in called genotypes"> ##INFO=<ID=DP4,Number=4,Description="Number of high-quality ref-forward,ref-reverse,alt-forward and alt-reverse bases"> ##INFO=<ID=MQ,Description="Average mapping quality"> ##bcftools_callVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c ##bcftools_callCommand=call -mv NA12878_snp_A2G_chr20_225058.vcf ##FILTER=<ID=LowQual,Description="Set if true: %QUAL<20 || DP>100"> ##bcftools_filterVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c ##bcftools_filterCommand=filter -s LowQual -e '%QUAL<20 || DP>100' NA12878_snp_A2G_chr20_225058.raw.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 20 224971 . G A 57 PASS DP=8;VDB=0.0132829;SGB=-0.556411;RPB=0.405132;MQB=1.01283;MQSB=1.01283;BQB=0.810265;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,4;MQ=60 GT:PL 0/1:90,70 20 225058 . A G 217 PASS DP=81;VDB=0.824099;SGB=-0.693139;RPB=0.952244;MQB=0.978845;MQSB=0.987634;BQB=3.33479e-07;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=25,14,21,15;MQ=59 GT:PL 0/1:250,255 与Avocado结果一致 参考： 附录中间结果： xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ bcftools view NA12878_snp_A2G_chr20_225058.variants ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##samtoolsVersion=1.3.1-24-gf458b7c+htslib-1.3.1-35-g481752c ##samtoolsCommand=samtools mpileup -vf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058.sorted.bam ##reference=file://Homo_sapiens_assembly19chr20.fasta ##contig=<ID=20,length=63025520> ##ALT=<ID=*,Description="Represents allele(s) other than observed."> ##INFO=<ID=INDEL,Description="Indicates that the variant is an INDEL."> ##INFO=<ID=IDV,Description="Maximum number of reads supporting an indel"> ##INFO=<ID=IMF,Description="Maximum fraction of reads supporting an indel"> ##INFO=<ID=DP,Description="Raw read depth"> ##INFO=<ID=VDB,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> ##INFO=<ID=RPB,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> ##INFO=<ID=MQB,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> ##INFO=<ID=BQB,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> ##INFO=<ID=MQSB,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> ##INFO=<ID=SGB,Description="Segregation based metric."> ##INFO=<ID=MQ0F,Description="Fraction of MQ0 reads (smaller is better)"> ##INFO=<ID=I16,Number=16,Description="Auxiliary tag used for calling,see description of bcf_callret1_t in bam2bcf.h"> ##INFO=<ID=QS,Number=R,Description="Auxiliary tag used for calling"> ##FORMAT=<ID=PL,Description="List of Phred-scaled genotype likelihoods"> ##bcftools_viewVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c ##bcftools_viewCommand=view NA12878_snp_A2G_chr20_225058.variants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 20 224959 . C <*> 0 . DP=1;I16=0,1,27,729,60,3600,0;QS=1,0;MQ0F=0 PL 0,3,27 20 224960 . A <*> 0 . DP=1;I16=0,33,1089,0;MQ0F=0 PL 0,33 20 224961 . T <*> 0 . DP=2;I16=0,2,54,1586,120,7200,4,0;MQ0F=0 PL 0,6,50 20 224962 . C <*> 0 . DP=4;I16=1,127,4041,240,14400,10,0;MQSB=1;MQ0F=0 PL 0,12,112 20 224963 . A <*> 0 . DP=4;I16=1,132,4358,8,22,115 20 224964 . G <*> 0 . DP=4;I16=1,4370,42,0;MQSB=1;MQ0F=0 PL 0,115 20 224965 . A <*> 0 . DP=5;I16=2,169,5737,300,18000,16,70,15,148 20 224966 . A <*> 0 . DP=5;I16=2,159,5191,21,107,0;MQSB=1;MQ0F=0 PL 0,139 20 224967 . A <*> 0 . DP=6;I16=2,195,6415,360,21600,26,154,18,160 20 224968 . A <*> 0 . DP=7;I16=3,231,7707,420,25200,32,212,0;MQSB=1.01283;MQ0F=0 PL 0,184 20 224969 . C <*> 0 . DP=7;I16=3,236,7980,39,283,188 20 224970 . T <*> 0 . DP=8;I16=3,245,8593,46,368,195 20 224971 . G A,<*> 0 . DP=8;I16=3,106,3746,139,4851,180,10800,126,35,341;QS=0.432653,0.567347,0;VDB=0.0132829;SGB=-0.556411;RPB=0.405132;MQB=1.01283;MQSB=1.01283;BQB=0.810265;MQ0F=0 PL 90,99,82,166 20 224972 . A <*> 0 . DP=8;I16=3,256,9364,580,202 20 224973 . G <*> 0 . DP=9;I16=4,5,303,10283,540,32400,716,0;MQSB=0.974597;MQ0F=0 PL 0,222 20 224974 . A <*> 0 . DP=10;I16=5,347,12087,600,36000,79,865,0;MQSB=0.952347;MQ0F=0 PL 0,30,245 20 224975 . A <*> 0 . DP=10;I16=5,345,12037,89,1033,0;MQSB=0.952347;MQ0F=0 PL 0,245 20 224976 . T <*> 0 . DP=11;I16=6,376,13014,660,39600,1221,0;MQSB=0.950952;MQ0F=0 PL 0,255 20 224977 . C <*> 0 . DP=12;I16=7,405,13713,720,43200,110,1430,0;MQSB=0.95494;MQ0F=0 PL 0,36,255 20 224978 . A <*> 0 . DP=12;I16=7,425,15099,122,1662,255 20 224979 . A <*> 0 . DP=12;I16=7,439,16071,134,1918,255 20 224980 . G <*> 0 . DP=15;I16=8,7,502,17056,900,54000,146,2198,45,255 20 224981 . G <*> 0 . DP=16;I16=9,542,18466,960,57600,161,2505,48,255 20 224982 . A <*> 0 . DP=16;I16=9,557,19493,177,2843,255 20 224983 . T <*> 0 . DP=16;I16=9,545,18627,193,3213,255 20 224984 . A <*> 0 . DP=17;I16=10,596,20950,1020,61200,209,3615,51,255 20 224985 . G <*> 0 . DP=17;I16=10,582,20016,225,3999,255 20 224986 . A <*> 0 . DP=19;I16=12,657,22891,1140,68400,241,4415,57,255 20 224987 . A <*> 0 . DP=19;I16=12,634,22430,1080,64800,251,4765,255 20 224988 . T <*> 0 . DP=21;I16=13,24646,1260,75600,273,5145,63,255 20 224989 . T <*> 0 . DP=21;I16=13,728,25366,290,5508,255 20 224990 . T <*> 0 . DP=23;I16=15,793,27491,1380,82800,307,5905,69,255 20 224991 . C <*> 0 . DP=23;I16=15,792,27322,325,6287,255 20 224992 . T <*> 0 . DP=23;I16=15,811,28691,343,6705,255 20 224993 . A <*> 0 . DP=25;I16=15,9,858,30696,1440,86400,7108,72,255 20 224994 . G <*> 0 . DP=27;I16=17,931,32225,1620,97200,388,7616,81,255 20 224995 . A <*> 0 . DP=28;I16=18,975,34429,1680,100800,408,8062,84,255 20 224996 . A <*> 0 . DP=29;I16=18,11,1010,35616,1740,104400,428,8498,0;MQSB=1;MQ0F=0 PL 0,87,255 20 224997 . A <*> 0 . DP=29;I16=18,1036,37180,449,8975,255 20 224998 . G <*> 0 . DP=30;I16=19,1007,34239,1800,108000,470,9494,90,255 20 224999 . T <*> 0 . DP=31;I16=20,1044,35740,1860,111600,491,10005,93,255 20 225000 . T <*> 0 . DP=33;I16=22,1105,38627,1920,115200,495,10219,96,255 20 225001 . C <*> 0 . DP=35;I16=24,1144,39032,2040,122400,517,10731,102,255 20 225002 . C <*> 0 . DP=35;I16=24,1179,41045,11238,255 20 225003 . T <*> 0 . DP=35;I16=24,1240,44402,2100,126000,12140,105,255 20 225004 . T <*> 0 . DP=37;I16=25,1238,43018,2160,129600,584,12286,108,255 20 225005 . C <*> 0 . DP=37;I16=25,1273,44191,2220,133200,630,13362,111,255 20 225006 . C <*> 0 . DP=37;I16=25,1281,44737,652,13894,255 20 225007 . C <*> 0 . DP=37;I16=25,1305,46243,673,14419,255 20 225008 . C <*> 0 . DP=39;I16=26,13,1347,46837,2340,140400,694,14986,117,255 20 225009 . T <*> 0 . DP=39;I16=26,1382,49302,15546,255 20 225010 . A <*> 0 . DP=39;I16=26,1375,48677,737,16099,255 20 225011 . A <*> 0 . DP=39;I16=25,50392,2280,136800,733,16069,114,255 20 225012 . A <*> 0 . DP=39;I16=26,1379,50223,752,16604,255 20 225013 . G <*> 0 . DP=39;I16=26,1334,46938,771,17177,255 20 225014 . C <*> 0 . DP=39;I16=26,1353,47331,813,18311,255 20 225015 . T <*> 0 . DP=40;I16=27,1417,50887,2400,144000,830,18854,255 20 225016 . T <*> 0 . DP=40;I16=27,1413,50181,846,19330,255 20 225017 . T <*> 0 . DP=40;I16=27,49151,837,19213,255 20 225018 . C <*> 0 . DP=41;I16=28,49427,2460,147600,878,20378,123,255 20 225019 . A <*> 0 . DP=44;I16=30,1489,52043,2580,154800,894,20900,129,255 20 225020 . C <*> 0 . DP=46;I16=31,1528,51118,2760,165600,921,21475,138,255 20 225021 . A <*> 0 . DP=48;I16=32,1588,54544,2820,169200,939,21935,141,255 20 225022 . C <*> 0 . DP=48;I16=32,1589,53249,2880,172800,967,22481,144,255 20 225023 . T <*> 0 . DP=49;I16=32,17,1731,61681,2940,176400,986,22984,148,255 20 225024 . T <*> 0 . DP=49;I16=32,1684,58626,1005,23475,255 20 225025 . G <*> 0 . DP=52;I16=34,1744,59236,3120,187200,1023,23953,157,255 20 225026 . C <*> 0 . DP=53;I16=35,1781,61425,1025,24079,255 20 225027 . C <*> 0 . DP=54;I16=36,1847,63779,3240,194400,1060,24720,163,255 20 225028 . T <*> 0 . DP=55;I16=37,1929,68767,3269,195241,1079,25109,0;MQSB=0.987054;MQ0F=0 PL 0,166,255 20 225029 . C <*> 0 . DP=55;I16=37,1884,65034,1099,25537,255 20 225030 . A <*> 0 . DP=58;I16=39,19,2019,70909,3449,206041,1117,25903,0;MQSB=0.98769;MQ0F=0 PL 0,175,255 20 225031 . G <*> 0 . DP=58;I16=39,1951,67385,3389,202441,1116,25824,0;MQSB=0.988135;MQ0F=0 PL 0,172,255 20 225032 . T <*> 0 . DP=59;I16=40,1975,67771,1136,26226,0;MQSB=0.988625;MQ0F=0 PL 0,255 20 225033 . G <*> 0 . DP=59;I16=40,1957,66637,1157,26669,255 20 225034 . T <*> 0 . DP=61;I16=41,2045,70271,3569,213241,1201,27677,0;MQSB=0.988669;MQ0F=0 PL 0,181,255 20 225035 . A <*> 0 . DP=61;I16=41,20,2108,73564,3629,216841,1245,28675,0;MQSB=0.988268;MQ0F=0 PL 0,184,255 20 225036 . T <*> 0 . DP=61;I16=41,2118,74190,1264,29090,255 20 225037 . A <*> 0 . DP=61;I16=41,2095,73559,1257,28873,255 20 225038 . T <*> 0 . DP=61;I16=41,2080,71942,1297,29801,255 20 225039 . A <*> 0 . DP=62;I16=42,2117,73267,3689,220441,1312,30150,0;MQSB=0.988726;MQ0F=0 PL 0,187,255 20 225040 . T <*> 0 . DP=62;I16=42,2133,75291,1303,29921,0;MQSB=0.989115;MQ0F=0 PL 0,255 20 225041 . G <*> 0 . DP=63;I16=42,2049,69025,1342,30890,255 20 225042 . T A,<*> 0 . DP=64;I16=42,2062,70408,28,784,1314,30096,25,625;QS=0.98659,0.01341,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=0.989158;BQB=1;MQ0F=0 PL 0,255,255 20 225043 . G <*> 0 . DP=64;I16=42,2144,73654,3749,224041,1354,31130,0;MQSB=0.98835;MQ0F=0 PL 0,190,255 20 225044 . G <*> 0 . DP=66;I16=43,2171,74097,3869,231241,1367,31493,0;MQSB=0.988439;MQ0F=0 PL 0,196,255 20 225045 . C <*> 0 . DP=68;I16=45,23,2260,76838,4049,242041,1405,32435,0;MQSB=0.98895;MQ0F=0 PL 0,205,255 20 225046 . T <*> 0 . DP=68;I16=45,2319,81177,32657,255 20 225047 . A <*> 0 . DP=68;I16=45,2256,76866,1428,32884,255 20 225048 . T <*> 0 . DP=68;I16=45,2228,75892,3989,238441,1414,32540,0;MQSB=0.989274;MQ0F=0 PL 0,202,255 20 225049 . A <*> 0 . DP=70;I16=46,2149,71849,3929,234841,1389,32189,0;MQSB=0.990313;MQ0F=0 PL 0,199,255 20 225050 . C <*> 0 . DP=70;I16=46,2229,73289,4109,245641,1457,33641,0;MQSB=0.989343;MQ0F=0 PL 0,208,255 20 225051 . C <*> 0 . DP=70;I16=45,24,2290,77206,4140,248400,1465,33883,255 20 225052 . A <*> 0 . DP=70;I16=45,2259,76893,1443,33309,255 20 225053 . C <*> 0 . DP=71;I16=46,2298,75208,4229,252841,1494,34560,0;MQSB=0.988741;MQ0F=0 PL 0,214,255 20 225054 . T <*> 0 . DP=71;I16=46,2410,83520,1496,34612,255 20 225055 . G <*> 0 . DP=71;I16=45,2336,78822,4169,249241,1475,34187,0;MQSB=0.988331;MQ0F=0 PL 0,211,255 20 225056 . A <*> 0 . DP=73;I16=46,2359,80979,1472,34088,0;MQSB=0.989038;MQ0F=0 PL 0,255 20 225057 . C <*> 0 . DP=77;I16=46,2183,68947,1510,35040,255 20 225058 . A G,<*> 0 . DP=81;I16=25,14,1348,46912,1002,28878,2129,126841,832,19188,766,17860;QS=0.573617,0.426383,0;VDB=0.824099;SGB=-0.693139;RPB=0.952244;MQB=0.978845;MQSB=0.987634;BQB=3.33479e-07;MQ0F=0 PL 250,255 20 225059 . G <*> 0 . DP=81;I16=46,2618,88958,4649,278041,1639,37793,0;MQSB=0.986878;MQ0F=0 PL 0,235,255 20 225060 . G <*> 0 . DP=80;I16=46,31,2500,83826,4589,274441,1626,37590,0;MQSB=0.987124;MQ0F=0 PL 0,232,255 20 225061 . C <*> 0 . DP=80;I16=47,2634,89812,4709,281641,1630,37550,0;MQSB=0.987315;MQ0F=0 PL 0,238,255 20 225062 . C <*> 0 . DP=79;I16=47,2470,79782,1624,37416,0;MQSB=0.987555;MQ0F=0 PL 0,255 20 225063 . G <*> 0 . DP=77;I16=46,69662,4529,270841,37340,0;MQSB=0.987376;MQ0F=0 PL 0,229,255 20 225064 . C <*> 0 . DP=77;I16=45,2616,91594,4469,267241,1592,36738,0;MQSB=0.986928;MQ0F=0 PL 0,226,255 20 225065 . C <*> 0 . DP=76;I16=45,2654,94076,36672,255 20 225066 . A <*> 0 . DP=75;I16=43,2614,94244,4349,260041,1569,36463,0;MQSB=0.985958;MQ0F=0 PL 0,220,255 20 225067 . G <*> 0 . DP=74;I16=43,2506,86398,1563,36431,255 20 225068 . T <*> 0 . DP=73;I16=43,29,2514,88542,4289,256441,1556,36352,0;MQSB=0.986238;MQ0F=0 PL 0,217,255 20 225069 . C <*> 0 . DP=72;I16=42,2473,86619,1549,36273,0;MQSB=0.985718;MQ0F=0 PL 0,255 20 225070 . A <*> 0 . DP=72;I16=42,2528,90620,1538,36044,255 20 225071 . T <*> 0 . DP=71;I16=42,2499,89623,1525,35713,0;MQSB=0.986014;MQ0F=0 PL 0,255 20 225072 . T <*> 0 . DP=71;I16=42,89435,1511,35379,255 20 225073 . A <*> 0 . DP=71;I16=42,2463,87069,1497,35093,255 20 225074 . A <*> 0 . DP=70;I16=41,2457,88171,1481,34705,0;MQSB=0.985472;MQ0F=0 PL 0,255 20 225075 . A <*> 0 . DP=69;I16=40,2449,88339,1463,34213,0;MQSB=0.984898;MQ0F=0 PL 0,255 20 225076 . T <*> 0 . DP=69;I16=40,2438,87596,33667,255 20 225077 . T <*> 0 . DP=69;I16=40,2439,87765,1421,33071,255 20 225078 . C <*> 0 . DP=68;I16=39,2329,81449,1400,32526,0;MQSB=0.984288;MQ0F=0 PL 0,255 20 225079 . A <*> 0 . DP=68;I16=39,2399,84889,32101,0;MQSB=0.983965;MQ0F=0 PL 0,255 20 225080 . A <*> 0 . DP=68;I16=39,2409,86149,1363,31435,255 20 225081 . G <*> 0 . DP=65;I16=38,2258,78780,1340,30822,0;MQSB=0.983981;MQ0F=0 PL 0,255 20 225082 . C <*> 0 . DP=64;I16=37,2204,76498,3809,227641,1318,30258,0;MQSB=0.983301;MQ0F=0 PL 0,255 20 225083 . T <*> 0 . DP=64;I16=37,2301,82983,1296,29742,255 20 225084 . C <*> 0 . DP=63;I16=37,2163,74877,1272,29124,0;MQSB=0.983665;MQ0F=0 PL 0,255 20 225085 . C <*> 0 . DP=62;I16=36,2107,72679,1247,28455,0;MQSB=0.982951;MQ0F=0 PL 0,255 20 225086 . A <*> 0 . DP=62;I16=36,2166,76070,1222,27836,255 20 225087 . A <*> 0 . DP=61;I16=35,2195,79377,1197,27217,0;MQSB=0.982188;MQ0F=0 PL 0,255 20 225088 . G <*> 0 . DP=61;I16=35,2092,72304,1171,26599,255 20 225089 . A <*> 0 . DP=59;I16=33,2054,73404,3480,208800,1122,25406,255 20 225090 . G <*> 0 . DP=59;I16=34,2000,68626,3509,209641,1123,25511,0;MQSB=0.981786;MQ0F=0 PL 0,178,255 20 225091 . A <*> 0 . DP=56;I16=32,1944,68122,3329,198841,1101,24987,0;MQSB=0.980457;MQ0F=0 PL 0,255 20 225092 . C <*> 0 . DP=56;I16=32,1867,62921,24507,255 20 225093 . A <*> 0 . DP=56;I16=32,1942,67998,1057,24071,255 20 225094 . A <*> 0 . DP=55;I16=32,1901,66367,1035,23629,0;MQSB=0.980932;MQ0F=0 PL 0,255 20 225095 . A <*> 0 . DP=53;I16=30,1815,62867,3149,188041,1013,23131,0;MQSB=0.978929;MQ0F=0 PL 0,160,255 20 225096 . C <*> 0 . DP=52;I16=29,1750,59286,3089,184441,989,22529,0;MQSB=0.977804;MQ0F=0 PL 0,255 20 225097 . T <*> 0 . DP=51;I16=29,1826,65594,3029,180841,965,21925,0;MQSB=0.978354;MQ0F=0 PL 0,255 20 225098 . C <*> 0 . DP=51;I16=29,60074,941,21369,255 20 225099 . T <*> 0 . DP=49;I16=28,1753,63097,2909,173641,918,20810,0;MQSB=0.977751;MQ0F=0 PL 0,255 20 225100 . T <*> 0 . DP=48;I16=27,1688,59612,2849,170041,896,20296,0;MQSB=0.976472;MQ0F=0 PL 0,255 20 225101 . G <*> 0 . DP=46;I16=25,1543,52049,2729,162841,873,19677,0;MQSB=0.973548;MQ0F=0 PL 0,255 20 225102 . A <*> 0 . DP=44;I16=23,1488,50652,2609,155641,850,19004,0;MQSB=0.970024;MQ0F=0 PL 0,255 20 225103 . A <*> 0 . DP=44;I16=23,1531,53697,826,18328,255 20 225104 . A <*> 0 . DP=44;I16=23,51873,801,17651,255 20 225105 . A <*> 0 . DP=41;I16=22,50294,2429,144841,779,17021,0;MQSB=0.969627;MQ0F=0 PL 0,255 20 225106 . A <*> 0 . DP=41;I16=22,1441,754,16288,255 20 225107 . A <*> 0 . DP=41;I16=22,49175,15556,255 20 225108 . A <*> 0 . DP=41;I16=22,701,14827,255 20 225109 . G <*> 0 . DP=39;I16=21,1278,42540,2309,137641,676,14150,0;MQSB=0.968368;MQ0F=0 PL 0,255 20 225110 . G <*> 0 . DP=37;I16=21,1262,43720,2189,130441,651,13423,0;MQSB=0.970373;MQ0F=0 PL 0,255 20 225111 . C <*> 0 . DP=37;I16=20,1211,41503,609,12457,255 20 225112 . A <*> 0 . DP=36;I16=21,45466,602,12118,0;MQSB=0.971458;MQ0F=0 PL 0,255 20 225113 . G <*> 0 . DP=35;I16=21,1219,42685,2069,123241,579,11537,0;MQSB=0.972604;MQ0F=0 PL 0,255 20 225114 . C <*> 0 . DP=35;I16=21,41303,556,11002,255 20 225115 . C <*> 0 . DP=35;I16=20,1178,41150,2009,119641,515,10175,0;MQSB=0.970446;MQ0F=0 PL 0,255 20 225116 . T <*> 0 . DP=33;I16=19,1173,41877,1949,116041,493,9717,0;MQSB=0.968015;MQ0F=0 PL 0,255 20 225117 . A <*> 0 . DP=33;I16=19,1141,40007,471,9303,255 20 225118 . G <*> 0 . DP=33;I16=19,1135,39339,447,8835,255 20 225119 . G <*> 0 . DP=32;I16=18,1090,37658,1889,112441,424,8414,0;MQSB=0.965264;MQ0F=0 PL 0,255 20 225120 . A <*> 0 . DP=30;I16=16,1031,35929,1769,105241,401,7939,0;MQSB=0.958545;MQ0F=0 PL 0,255 20 225121 . G <*> 0 . DP=27;I16=15,31436,94441,379,7409,0;MQSB=0.958048;MQ0F=0 PL 0,255 20 225122 . A <*> 0 . DP=26;I16=14,851,28365,1529,90841,358,6922,0;MQSB=0.953497;MQ0F=0 PL 0,78,255 20 225123 . A <*> 0 . DP=26;I16=14,887,30579,337,6477,255 20 225124 . A <*> 0 . DP=25;I16=14,30767,1469,87241,316,6024,0;MQSB=0.955682;MQ0F=0 PL 0,75,255 20 225125 . G <*> 0 . DP=25;I16=14,824,27454,293,5515,255 20 225126 . C <*> 0 . DP=22;I16=12,717,23833,1289,76441,5049,0;MQSB=0.947103;MQ0F=0 PL 0,66,255 20 225127 . A <*> 0 . DP=20;I16=11,671,22767,1169,69241,4621,0;MQSB=0.943233;MQ0F=0 PL 0,255 20 225128 . A <*> 0 . DP=19;I16=10,641,21917,1109,65641,4228,0;MQSB=0.934728;MQ0F=0 PL 0,255 20 225129 . C <*> 0 . DP=18;I16=9,589,19515,221,3819,255 20 225130 . A <*> 0 . DP=18;I16=8,20190,192,3300,255 20 225131 . T <*> 0 . DP=14;I16=6,482,16740,840,50400,179,2979,255 20 225132 . G <*> 0 . DP=13;I16=6,15479,780,46800,167,2683,0;MQSB=0.961166;MQ0F=0 PL 0,255 20 225133 . A <*> 0 . DP=13;I16=6,454,15926,155,2411,255 20 225134 . T <*> 0 . DP=13;I16=6,433,14821,142,2114,255 20 225135 . T <*> 0 . DP=11;I16=5,390,13926,131,1841,0;MQSB=0.950952;MQ0F=0 PL 0,255 20 225136 . T <*> 0 . DP=11;I16=5,387,13697,1590,255 20 225137 . T <*> 0 . DP=11;I16=5,391,14009,109,1361,255 20 225138 . T <*> 0 . DP=11;I16=5,386,13644,98,1154,255 20 225139 . C <*> 0 . DP=11;I16=5,12000,969,0;MQSB=0.950952;MQ0F=0 PL 0,246 20 225140 . A <*> 0 . DP=10;I16=4,351,12335,77,805,0;MQSB=1.00775;MQ0F=0 PL 0,243 20 225141 . C <*> 0 . DP=10;I16=4,335,11279,67,661,236 20 225142 . A <*> 0 . DP=10;I16=4,11809,537,238 20 225143 . T <*> 0 . DP=9;I16=4,302,10172,432,220 20 225144 . A <*> 0 . DP=9;I16=4,294,9686,0;MQSB=0.974597;MQ0F=0 PL 0,216 20 225145 . T <*> 0 . DP=7;I16=4,7565,274,183 20 225146 . T <*> 0 . DP=5;I16=2,174,6066,215,150 20 225147 . T <*> 0 . DP=5;I16=2,5936,150 20 225148 . T <*> 0 . DP=5;I16=2,164,5392,141 20 225149 . A <*> 0 . DP=4;I16=2,125,3931,97,114 20 225150 . A <*> 0 . DP=2;I16=1,2385,73,69 20 225151 . C <*> 0 . DP=2;I16=1,68,2312,53,68 20 225152 . T <*> 0 . DP=2;I16=1,2452,37,70 20 225153 . T <*> 0 . DP=2;I16=1,63 20 225154 . G <*> 0 . DP=1;I16=1,34,1156,34 20 225155 . G <*> 0 . DP=1;I16=1,34 20 225156 . T <*> 0 . DP=1;I16=1,841,29 20 225157 . T <*> 0 . DP=1;I16=1,26 20 225158 . T <*> 0 . DP=1;I16=1,576,24 xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ bcftools （编辑：东莞站长网） 【声明】本站内容均来自网络，其相关言论仅代表作者个人观点，不代表本站立场。若无意侵犯到您的权利，请及时与联系站长删除相关内容! |
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