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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 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_

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_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。

  1. 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:
【1】 http://www.htslib.org/doc/samtools.html

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

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