VSIM Tool

Personal Interpretation

Visualization

Result:

Table Format:

Input: VCF files

##fileformat=VCFv4.2
##ALT=<ID=DEL,Description="Deletion">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
##reference=GRCh37
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096
1	30923	rs140337953	G	T	100	PASS	AA=T;AC=1584;AF=0.73;AFR_AF=0.48;AMR_AF=0.80;AN=2184;ASN_AF=0.89;AVGPOST=0.7335;ERATE=0.0183;EUR_AF=0.73;LDAF=0.6576;RSQ=0.5481;SNPSOURCE=LOWCOV;THETA=0.0162;VT=SNP	GT:DS:PL	1|1:1.750:49,5,0
1	51479	rs116400033	T	A	100	PASS	AA=T;AC=235;AF=0.11;AFR_AF=0.03;AMR_AF=0.16;AN=2184;ASN_AF=0.0035;AVGPOST=0.9085;ERATE=0.0012;EUR_AF=0.22;LDAF=0.1404;RSQ=0.7414;SNPSOURCE=LOWCOV;THETA=0.0131;VT=SNP	GT:DS:PL	1|1:1.450:49,5,0
1	52058	rs62637813	G	C	100	PASS	AA=C;AC=64;AF=0.03;AFR_AF=0.02;AMR_AF=0.04;AN=2184;ASN_AF=0.0017;AVGPOST=0.9264;ERATE=0.0057;EUR_AF=0.05;LDAF=0.0620;RSQ=0.4882;SNPSOURCE=LOWCOV;THETA=0.0069;VT=SNP	GT:DS:PL	0|1:0.850:19,0,37
1	52238	rs150021059	T	G	100	PASS	AA=G;AC=1941;AF=0.89;AFR_AF=0.64;AMR_AF=0.93;AN=2184;ASN_AF=0.99;AVGPOST=0.8617;ERATE=0.0026;EUR_AF=0.95;LDAF=0.8423;RSQ=0.6256;SNPSOURCE=LOWCOV;THETA=0.0132;VT=SNP	GT:DS:PL	1|1:2.000:50,19,0
1	54490	rs141149254	G	A	100	PASS	AA=G;AC=175;AF=0.08;AFR_AF=0.03;AMR_AF=0.12;AN=2184;ASN_AF=0.0035;AVGPOST=0.9646;ERATE=0.0004;EUR_AF=0.15;LDAF=0.0929;RSQ=0.8366;SNPSOURCE=LOWCOV;THETA=0.0074;VT=SNP	GT:DS:PL	1|0:1.000:50,0,42
1	54676	rs2462492	C	T	100	PASS	AA=T;AC=267;AF=0.12;AFR_AF=0.09;AMR_AF=0.20;AN=2184;ASN_AF=0.02;AVGPOST=0.8998;ERATE=0.0037;EUR_AF=0.18;LDAF=0.1528;RSQ=0.6989;SNPSOURCE=LOWCOV;THETA=0.0110;VT=SNP	GT:DS:PL	0|1:1.000:26,0,17
1	55164	rs3091274	C	A	100	PASS	AA=A;AC=1955;AF=0.90;AFR_AF=0.65;AMR_AF=0.94;AN=2184;ASN_AF=0.99;AVGPOST=0.8686;ERATE=0.0045;EUR_AF=0.96;LDAF=0.8489;RSQ=0.6373;SNPSOURCE=LOWCOV;THETA=0.0162;VT=SNP	GT:DS:PL	1|1:1.900:25,2,0
1	57952	rs189727433	A	C	100	PASS	AA=C;AC=1902;AF=0.87;AFR_AF=0.64;AMR_AF=0.91;AN=2184;ASN_AF=0.98;AVGPOST=0.7578;ERATE=0.0085;EUR_AF=0.91;LDAF=0.7878;RSQ=0.4712;SNPSOURCE=LOWCOV;THETA=0.0076;VT=SNP	GT:DS:PL	1|1:1.950:26,3,0
1	61442	rs74970982	A	G	100	PASS	AA=G;AC=2084;AF=0.95;AFR_AF=0.84;AMR_AF=0.97;AN=2184;ASN_AF=1.00;AVGPOST=0.9004;ERATE=0.0026;EUR_AF=0.99;LDAF=0.9152;RSQ=0.4867;SNPSOURCE=LOWCOV;THETA=0.0013;VT=SNP	GT:DS:PL	1|1:2.000:26,3,0
1	63735	rs201888535	CCTA	C	455	PASS	AA=CCTA;AC=829;AF=0.38;AFR_AF=0.13;AMR_AF=0.33;AN=2184;ASN_AF=0.69;AVGPOST=0.7654;ERATE=0.0047;EUR_AF=0.34;LDAF=0.4128;RSQ=0.6424;THETA=0.0062;VT=INDEL	GT:DS:PL	1|1:1.750:150,9,0
1	66162	rs62639105	A	T	100	PASS	AA=.;AC=544;AF=0.25;AFR_AF=0.23;AMR_AF=0.30;AN=2184;ASN_AF=0.07;AVGPOST=0.7777;ERATE=0.0166;EUR_AF=0.38;LDAF=0.3089;RSQ=0.5681;SNPSOURCE=LOWCOV;THETA=0.0026;VT=SNP	GT:DS:PL	0|1:0.950:18,0,36
1	66507	rs12401368	T	A	100	PASS	AA=.;AC=170;AF=0.08;AFR_AF=0.05;AMR_AF=0.09;AN=2184;ASN_AF=0.07;AVGPOST=0.6536;ERATE=0.0197;EUR_AF=0.09;LDAF=0.2457;RSQ=0.2110;SNPSOURCE=LOWCOV;THETA=0.0122;VT=SNP	GT:DS:PL	0|1:1.000:23,0,17
1	69511	rs75062661	A	G	100	PASS	AA=.;AC=1424;AF=0.65;AFR_AF=0.33;AMR_AF=0.65;AN=2184;ASN_AF=0.87;AVGPOST=0.7173;ERATE=0.0237;EUR_AF=0.70;LDAF=0.6051;RSQ=0.5669;SNPSOURCE=LOWCOV;THETA=0.0052;VT=SNP	GT:DS:PL	1|1:1.600:31,3,0
1	73841	rs143773730	C	T	100	PASS	AA=.;AC=425;AF=0.19;AFR_AF=0.17;AMR_AF=0.22;AN=2184;ASN_AF=0.15;AVGPOST=0.8178;ERATE=0.0303;EUR_AF=0.23;LDAF=0.2588;RSQ=0.5832;SNPSOURCE=LOWCOV;THETA=0.0044;VT=SNP	GT:DS:PL	0|1:1.000:47,0,14
1	79033	rs62641298	A	G	100	PASS	AA=.;AC=1961;AF=0.90;AFR_AF=0.65;AMR_AF=0.95;AN=2184;ASN_AF=0.98;AVGPOST=0.7371;ERATE=0.0054;EUR_AF=0.97;LDAF=0.7962;RSQ=0.3963;SNPSOURCE=LOWCOV;THETA=0.0022;VT=SNP	GT:DS:PL	1|1:1.900:0,0,0
1	79050	rs62641299	G	T	100	PASS	AA=.;AC=1871;AF=0.86;AFR_AF=0.54;AMR_AF=0.93;AN=2184;ASN_AF=0.98;AVGPOST=0.6803;ERATE=0.0107;EUR_AF=0.94;LDAF=0.7318;RSQ=0.3928;SNPSOURCE=LOWCOV;THETA=0.0031;VT=SNP	GT:DS:PL	1|1:1.650:0,0,0
1	83084	rs181193408	T	A	100	PASS	AA=.;AC=1914;AF=0.88;AFR_AF=0.58;AMR_AF=0.92;AN=2184;ASN_AF=0.99;AVGPOST=0.8261;ERATE=0.0061;EUR_AF=0.96;LDAF=0.8278;RSQ=0.5750;SNPSOURCE=LOWCOV;THETA=0.0064;VT=SNP	GT:DS:PL	1|1:1.850:29,3,0
1	84002	rs28850140	G	A	100	PASS	AA=.;AC=236;AF=0.11;AFR_AF=0.07;AMR_AF=0.15;AN=2184;ASN_AF=0.12;AVGPOST=0.8144;ERATE=0.0211;EUR_AF=0.11;LDAF=0.1921;RSQ=0.4810;SNPSOURCE=LOWCOV;THETA=0.0050;VT=SNP	GT:DS:PL	0|1:1.000:50,0,31
1	84005	rs202079949	AG	A	78	PASS	AA=.;AC=52;AF=0.02;AFR_AF=0.02;AMR_AF=0.03;AN=2184;ASN_AF=0.01;AVGPOST=0.9360;ERATE=0.0049;EUR_AF=0.04;LDAF=0.0514;RSQ=0.4690;THETA=0.0005;VT=INDEL	GT:DS:PL	1|0:1.000:68,0,26
1	89946	rs138808727	A	T	100	PASS	AA=.;AC=236;AF=0.11;AFR_AF=0.02;AMR_AF=0.16;AN=2184;ASN_AF=0.0035;AVGPOST=0.9001;ERATE=0.0009;EUR_AF=0.22;LDAF=0.1417;RSQ=0.7414;SNPSOURCE=LOWCOV;THETA=0.0100;VT=SNP	GT:DS:PL	1|1:1.950:50,9,0
1	91536	rs77418980	G	T	100	PASS	AA=.;AC=695;AF=0.32;AFR_AF=0.04;AMR_AF=0.30;AN=2184;ASN_AF=0.34;AVGPOST=0.7792;ERATE=0.0025;EUR_AF=0.50;LDAF=0.3255;RSQ=0.6634;SNPSOURCE=LOWCOV;THETA=0.0018;VT=SNP	GT:DS:PL	1|1:1.400:0,0,0
1	91581	rs151118460	G	A	100	PASS	AA=.;AC=716;AF=0.33;AFR_AF=0.04;AMR_AF=0.30;AN=2184;ASN_AF=0.37;AVGPOST=0.7763;ERATE=0.0035;EUR_AF=0.50;LDAF=0.3353;RSQ=0.6618;SNPSOURCE=LOWCOV;THETA=0.0078;VT=SNP	GT:DS:PL	1|1:1.350:0,0,0
1	92858	rs147061536	G	T	100	PASS	AA=.;AC=248;AF=0.11;AFR_AF=0.05;AMR_AF=0.15;AN=2184;ASN_AF=0.01;AVGPOST=0.9072;ERATE=0.0046;EUR_AF=0.22;LDAF=0.1433;RSQ=0.7567;SNPSOURCE=LOWCOV;THETA=0.0212;VT=SNP	GT:DS:PL	1|1:1.750:28,3,0

Full VCF file you can find it here: ExampleFile.vcf

This file created from the sequence data of the human genomes collected from 1000 Genomes Project The VCF files have all the individual's information for each chromosome. By using Jvarkit we extracted individual VCF files from the main VCF file for all the chromosomes. We then concatenated the chromosomes list for each individual using VCFtool to generate a single VCF file containing all the information of one individual.

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