##fileformat=VCFv4.1
##samtoolsVersion=0.1.19-44428cd
##reference=file:///home/epushkova/AB/chr17.fa
##contig=<ID=chr17,length=81195210>
##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 first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##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=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##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.">
##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias">
##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken.">
##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=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	/home/epushkova/AB/OUT_10.bam
chr17	41197661	.	G	A	6.95	.	DP=3;VDB=2.309944e-02;AF1=1;AC1=2;DP4=0,0,1,2;MQ=60;FQ=-36	GT:PL:GQ	1/1:38,9,0:10
chr17	41215890	.	C	A	29.8	.	DP=2;VDB=5.960000e-02;AF1=1;AC1=2;DP4=0,0,1,1;MQ=60;FQ=-33	GT:PL:GQ	1/1:61,6,0:10
chr17	41222881	.	T	G	14.1	.	DP=3;VDB=2.309944e-02;AF1=1;AC1=2;DP4=0,0,2,1;MQ=60;FQ=-36	GT:PL:GQ	1/1:46,9,0:14
chr17	41223291	.	A	C	43.5	.	DP=4;VDB=1.106034e-02;AF1=1;AC1=2;DP4=0,0,2,2;MQ=60;FQ=-39	GT:PL:GQ	1/1:76,12,0:21
chr17	41228456	.	T	G	27.3	.	DP=5;VDB=5.617677e-03;AF1=1;AC1=2;DP4=0,0,1,4;MQ=60;FQ=-42	GT:PL:GQ	1/1:60,15,0:27
chr17	41256841	.	AT	A	29.2	.	INDEL;IS=2,1.000000;DP=2;VDB=7.840000e-02;AF1=1;AC1=2;DP4=0,0,2,0;MQ=60;FQ=-40.5	GT:PL:GQ	1/1:68,6,0:10
chr17	41320145	.	CATATA	CATA	95	.	INDEL;IS=4,1.000000;DP=4;VDB=1.165196e-02;AF1=1;AC1=2;DP4=0,0,1,3;MQ=60;FQ=-46.5	GT:PL:GQ	1/1:135,12,0:21