view vcf/father.vcf @ 0:05c27700e5ca

initial commit

##fileformat=VCFv4.1
##samtoolsVersion=0.1.19-44428cd
##reference=file:///Users/alice/programs/galaxy/galaxy-dist/database/files/000/dataset_340.dat
##contig=<ID=comp0_c0_seq1,length=1035>
##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	/Users/alice/programs/galaxy/galaxy-dist/database/files/000/dataset_339.dat
comp0_c0_seq1	672	.	A	C	99.5	.	DP=4;VDB=6.376843e-02;AF1=1;AC1=2;DP4=0,0,2,2;MQ=60;FQ=-39	GT:PL:GQ	1/1:132,12,0:21
comp0_c0_seq1	706	.	C	G	131	.	DP=8;VDB=9.321602e-02;AF1=1;AC1=2;DP4=0,0,3,3;MQ=47;FQ=-45	GT:PL:GQ	1/1:164,18,0:33
comp0_c0_seq1	907	.	CAAA	CAAAA	114	.	INDEL;IS=6,0.857143;DP=7;VDB=1.075274e-01;AF1=1;AC1=2;DP4=0,0,1,6;MQ=57;FQ=-55.5	GT:PL:GQ	1/1:154,21,0:39
comp0_c0_seq1	966	.	A	C	90.1	.	DP=6;VDB=5.992091e-02;AF1=1;AC1=2;DP4=0,0,0,6;MQ=52;FQ=-45	GT:PL:GQ	1/1:123,18,0:33