forked from jdoughertyii/PyVCF
/
samtools.vcf
34 lines (34 loc) · 3.53 KB
/
samtools.vcf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
##fileformat=VCFv4.1
##samtoolsVersion=0.1.16 (r963:234)
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT -
chrX 2774478 . A G 61.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=60;FQ=-42 GT:PL:GQ 1/1:94,15,0:27
chrX 2832661 . A T 29 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=14,1,6,1;MQ=56;FQ=32;PV4=1,0.00034,0.00019,1 GT:PL:GQ 0/1:59,0,144:62
chrX 2832880 . AAT AATAT 109 . INDEL;DP=20;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,8;MQ=47;FQ=112;PV4=1,1,0.0069,0.091 GT:PL:GQ 0/1:147,0,172:99
chrX 2832920 . TTAT TTATAT 85.5 . INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,5;MQ=56;FQ=88.5;PV4=1,0.36,0.052,0.017 GT:PL:GQ 0/1:123,0,150:99
chrX 2833534 . TTACGCCCT T 8.18 . INDEL;DP=15;AF1=0.5;CI95=0.5,0.5;DP4=10,0,2,0;MQ=60;FQ=10.8;PV4=1,0.0041,1,0.3 GT:PL:GQ 0/1:45,0,255:47
chrX 2833580 . A G 80 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=10,2,7,1;MQ=58;FQ=83;PV4=1,1,0.06,1 GT:PL:GQ 0/1:110,0,141:99
chr1 10363194 . cca cCAca 57.5 . INDEL;DP=19;AF1=0.5;CI95=0.5,0.5;DP4=16,0,3,0;MQ=59;FQ=60.5;PV4=1,1,1,0.0008 GT:PL:GQ 0/1:95,0,214:98
chr1 11292952 . T A,C 41 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=57;FQ=-75 GT:PL:GQ 1/1:74,48,0,66,28,63:85
chr1 38304491 . t tTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTT,tTTTTTTT 16.3 . INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41;FQ=-40.5 GT:PL:GQ 1/1:105,56,50,54,0,51,98,45,44,95:10
chr1 152195728 . ATTTTTTTTTTT ATTTTTTTTTT,ATTTTTTTTT 36.5 . INDEL;DP=39;AF1=1;CI95=1,1;DP4=1,1,12,19;MQ=59;FQ=-104;PV4=1,0.42,0.4,0.2 GT:PL:GQ 1/1:77,69,0,77,75,73:99
chr1 152276149 . C T 134 . DP=30;AF1=0.5;CI95=0.5,0.5;DP4=2,7,8,11;MQ=33;FQ=45;PV4=0.42,0.23,0.33,1 GT:PL:GQ 0/1:164,0,72:75