VSIM Tool

Premarital Testing

Visualization

Result:

Table Format:

Input1: Mother 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	mother
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|1:1.950:49,8,0
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|1:2.000:49,6,0
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|1:1.000:50,0,14
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|1:1.950:26,2,0
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|1:1.800:0,0,0
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|1:2.000:29,3,0
1	61987	rs76735897	A	G	100	PASS	AA=A;AC=569;AF=0.26;AFR_AF=0.25;AMR_AF=0.31;AN=2184;ASN_AF=0.07;AVGPOST=0.8533;ERATE=0.0012;EUR_AF=0.39;LDAF=0.2944;RSQ=0.7192;SNPSOURCE=LOWCOV;THETA=0.0015;VT=SNP	GT:DS:PL	0|1:1.000:24,0,17
1	61989	rs77573425	G	C	100	PASS	AA=G;AC=555;AF=0.25;AFR_AF=0.22;AMR_AF=0.31;AN=2184;ASN_AF=0.07;AVGPOST=0.8584;ERATE=0.0007;EUR_AF=0.39;LDAF=0.2849;RSQ=0.7254;SNPSOURCE=LOWCOV;THETA=0.0019;VT=SNP	GT:DS:PL	0|1:1.000:24,0,17
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|0:1.200:100,6,0
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|1:1.000:47,0,14
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|0:1.450:24,2,0
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|1:1.800:0,0,0
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|1:1.700:0,0,0
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|1:2.000:31,3,0
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	0|1:1.100:0,0,0
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	0|1:1.300:0,0,0
1	120705	rs4117992	T	C	100	PASS	AA=.;AC=2000;AF=0.92;AFR_AF=0.74;AMR_AF=0.95;AN=2184;ASN_AF=0.97;AVGPOST=0.6866;ERATE=0.0100;EUR_AF=0.97;LDAF=0.7775;RSQ=0.2671;SNPSOURCE=LOWCOV;THETA=0.0304;VT=SNP	GT:DS:PL	1|1:1.800:0,0,0
1	120983	rs182468771	C	T	100	PASS	AA=.;AC=133;AF=0.06;AFR_AF=0.04;AMR_AF=0.09;AN=2184;ASN_AF=0.03;AVGPOST=0.7375;ERATE=0.0122;EUR_AF=0.09;LDAF=0.1947;RSQ=0.3091;SNPSOURCE=LOWCOV;THETA=0.0225;VT=SNP	GT:DS:PL	1|0:1.000:40,0,50
1	121009	rs1851943	C	T	100	PASS	AA=.;AC=464;AF=0.21;AFR_AF=0.26;AMR_AF=0.27;AN=2184;ASN_AF=0.13;AVGPOST=0.6419;ERATE=0.0237;EUR_AF=0.22;LDAF=0.3572;RSQ=0.3182;SNPSOURCE=LOWCOV;THETA=0.0113;VT=SNP	GT:DS:PL	1|0:1.000:50,0,50
1	126108	rs146756510	G	A	100	PASS	AA=.;AC=126;AF=0.06;AFR_AF=0.08;AMR_AF=0.13;AN=2184;ASN_AF=0.01;AVGPOST=0.9469;ERATE=0.0023;EUR_AF=0.04;LDAF=0.0781;RSQ=0.6899;SNPSOURCE=LOWCOV;THETA=0.0038;VT=SNP	GT:DS:PL	1|0:1.000:35,0,50
1	126113	rs79114531	C	A	100	PASS	AA=.;AC=2069;AF=0.95;AFR_AF=0.79;AMR_AF=0.97;AN=2184;ASN_AF=1.00;AVGPOST=0.9450;ERATE=0.0024;EUR_AF=1.00;LDAF=0.9281;RSQ=0.6875;SNPSOURCE=LOWCOV;THETA=0.0151;VT=SNP	GT:DS:PL	1|1:2.000:50,23,0
1	135032	rs148209574	G	A	100	PASS	AA=.;AC=155;AF=0.07;AFR_AF=0.10;AMR_AF=0.14;AN=2184;ASN_AF=0.01;AVGPOST=0.9468;ERATE=0.0036;EUR_AF=0.07;LDAF=0.0898;RSQ=0.7186;SNPSOURCE=LOWCOV;THETA=0.0181;VT=SNP	GT:DS:PL	1|0:1.000:50,0,50
1	534192	rs6680723	C	T	100	PASS	AA=T;AC=469;AF=0.21;AFR_AF=0.23;AMR_AF=0.29;AN=2184;ASN_AF=0.17;AVGPOST=0.8367;ERATE=0.0182;EUR_AF=0.20;LDAF=0.2793;RSQ=0.5894;SNPSOURCE=LOWCOV;THETA=0.0250;VT=SNP	GT:DS:PL	0|1:1.000:50,0,50
1	534198	rs6680725	C	T	100	PASS	AA=T;AC=236;AF=0.11;AFR_AF=0.22;AMR_AF=0.10;AN=2184;ASN_AF=0.07;AVGPOST=0.9211;ERATE=0.0152;EUR_AF=0.07;LDAF=0.1352;RSQ=0.7061;SNPSOURCE=LOWCOV;THETA=0.0057;VT=SNP	GT:DS:PL	1|0:0.900:26,0,50
1	563625	rs191286235	T	C	100	PASS	AA=C;AC=2115;AF=0.97;AFR_AF=0.95;AMR_AF=0.98;AN=2184;ASN_AF=0.98;AVGPOST=0.6693;ERATE=0.0152;EUR_AF=0.97;LDAF=0.7973;RSQ=0.1227;SNPSOURCE=LOWCOV;THETA=0.0122;VT=SNP	GT:DS:PL	1|1:1.750:0,0,0
1	691541	rs201999089	AT	A	93	PASS	AA=.;AC=259;AF=0.12;AFR_AF=0.04;AMR_AF=0.22;AN=2184;ASN_AF=0.05;AVGPOST=0.7781;ERATE=0.0039;EUR_AF=0.18;LDAF=0.2044;RSQ=0.4763;THETA=0.0064;VT=INDEL	GT:DS:PL	0|1:1.000:22,0,144
1	701946	rs149754976	A	G	100	PASS	AA=.;AC=1739;AF=0.80;AFR_AF=0.88;AMR_AF=0.84;AN=2184;ASN_AF=0.51;AVGPOST=0.7212;ERATE=0.0141;EUR_AF=0.94;LDAF=0.7186;RSQ=0.5135;SNPSOURCE=LOWCOV;THETA=0.0047;VT=SNP	GT:DS:PL	1|1:1.900:49,5,0
1	704367	rs71507456	T	C	100	PASS	AA=.;AC=1887;AF=0.86;AFR_AF=0.92;AMR_AF=0.90;AN=2184;ASN_AF=0.67;AVGPOST=0.7707;ERATE=0.0088;EUR_AF=0.95;LDAF=0.7833;RSQ=0.5129;SNPSOURCE=LOWCOV;THETA=0.0055;VT=SNP	GT:DS:PL	1|1:1.950:49,8,0
1	706368	rs55727773	A	G	100	PASS	AA=.;AC=606;AF=0.28;AFR_AF=0.04;AMR_AF=0.42;AN=2184;ASN_AF=0.20;AVGPOST=0.8669;ERATE=0.0054;EUR_AF=0.42;LDAF=0.3039;RSQ=0.7695;SNPSOURCE=LOWCOV;THETA=0.0074;VT=SNP	GT:DS:PL	0|1:1.100:47,0,13
1	714427	rs12028261	G	A	100	PASS	AA=.;AC=1753;AF=0.80;AFR_AF=0.49;AMR_AF=0.88;AN=2184;ASN_AF=0.79;AVGPOST=0.9238;ERATE=0.0035;EUR_AF=0.98;LDAF=0.7973;RSQ=0.8340;SNPSOURCE=LOWCOV;THETA=0.0040;VT=SNP	GT:DS:PL	1|1:2.000:49,5,0
1	715348	rs3131984	T	G	100	PASS	AA=.;AC=2184;AF=1.00;AFR_AF=1.00;AMR_AF=1.00;AN=2184;ASN_AF=1.00;AVGPOST=0.9974;ERATE=0.0006;EUR_AF=1.00;LDAF=0.9987;RSQ=0.1317;SNPSOURCE=LOWCOV;THETA=0.0031;VT=SNP	GT:DS:PL	1|1:2.000:31,3,0
1	718555	rs10751453	T	C	100	PASS	AA=.;AC=2169;AF=0.99;AFR_AF=0.99;AMR_AF=0.99;AN=2184;ASN_AF=1.00;AVGPOST=0.9713;ERATE=0.0048;EUR_AF=1.00;LDAF=0.9817;RSQ=0.3711;SNPSOURCE=LOWCOV;THETA=0.0018;VT=SNP	GT:DS:PL	1|1:1.950:0,0,0
1	720240	rs3121393	T	C	100	PASS	AA=.;AC=2021;AF=0.93;AFR_AF=0.95;AMR_AF=0.93;AN=2184;ASN_AF=0.81;AVGPOST=0.9832;ERATE=0.0008;EUR_AF=0.99;LDAF=0.9212;RSQ=0.9143;SNPSOURCE=LOWCOV;THETA=0.0015;VT=SNP	GT:DS:PL	1|1:2.000:0,0,0
1	720797	rs75530702	G	A	100	PASS	AA=.;AC=2027;AF=0.93;AFR_AF=0.95;AMR_AF=0.93;AN=2184;ASN_AF=0.82;AVGPOST=0.9828;ERATE=0.0018;EUR_AF=1.00;LDAF=0.9224;RSQ=0.9089;SNPSOURCE=LOWCOV;THETA=0.0022;VT=SNP	GT:DS:PL	1|1:2.000:49,8,0
1	723891	rs2977670	G	C	100	PASS	AA=.;AC=1720;AF=0.79;AFR_AF=0.50;AMR_AF=0.86;AN=2184;ASN_AF=0.78;AVGPOST=0.9930;ERATE=0.0012;EUR_AF=0.95;LDAF=0.7873;RSQ=0.9857;SNPSOURCE=LOWCOV;THETA=0.0009;VT=SNP	GT:DS:PL	1|1:2.000:50,14,0
1	728159	rs3131978	C	T	100	PASS	AA=.;AC=1995;AF=0.91;AFR_AF=0.94;AMR_AF=0.92;AN=2184;ASN_AF=0.78;AVGPOST=0.9390;ERATE=0.0059;EUR_AF=0.99;LDAF=0.8943;RSQ=0.7769;SNPSOURCE=LOWCOV;THETA=0.0032;VT=SNP	GT:DS:PL	1|1:2.000:18,2,0
1	728242	rs3131977	C	G	100	PASS	AA=.;AC=2005;AF=0.92;AFR_AF=0.93;AMR_AF=0.92;AN=2184;ASN_AF=0.80;AVGPOST=0.9647;ERATE=0.0017;EUR_AF=1.00;LDAF=0.9074;RSQ=0.8511;SNPSOURCE=LOWCOV;THETA=0.0015;VT=SNP	GT:DS:PL	1|1:2.000:50,10,0
1	729679	rs4951859	C	G	100	PASS	AA=.;AC=1440;AF=0.66;AFR_AF=0.31;AMR_AF=0.77;AN=2184;ASN_AF=0.65;AVGPOST=0.9514;ERATE=0.0009;EUR_AF=0.83;LDAF=0.6596;RSQ=0.9300;SNPSOURCE=LOWCOV;THETA=0.0010;VT=SNP	GT:DS:PL	1|1:2.000:49,8,0
1	732134	rs201400700	T	TA	176	PASS	AA=T;AC=28;AF=0.01;AFR_AF=0.0041;AMR_AF=0.06;AN=2184;AVGPOST=0.9911;ERATE=0.0005;EUR_AF=0.01;LDAF=0.0169;RSQ=0.7966;THETA=0.0019;VT=INDEL	GT:DS:PL	0|1:1.000:63,0,20
1	733998	rs61770164	C	T	100	PASS	AA=.;AC=1932;AF=0.88;AFR_AF=0.88;AMR_AF=0.90;AN=2184;ASN_AF=0.75;AVGPOST=0.9090;ERATE=0.0043;EUR_AF=0.98;LDAF=0.8600;RSQ=0.7507;SNPSOURCE=LOWCOV;THETA=0.0062;VT=SNP	GT:DS:PL	1|1:1.900:0,0,0
1	734042	rs61770165	G	A	100	PASS	AA=.;AC=1946;AF=0.89;AFR_AF=0.90;AMR_AF=0.91;AN=2184;ASN_AF=0.74;AVGPOST=0.8950;ERATE=0.0056;EUR_AF=0.99;LDAF=0.8577;RSQ=0.7284;SNPSOURCE=LOWCOV;THETA=0.0018;VT=SNP	GT:DS:PL	1|1:2.000:31,3,0
1	734462	rs12564807	G	A	100	PASS	AA=.;AC=1606;AF=0.74;AFR_AF=0.66;AMR_AF=0.72;AN=2184;ASN_AF=0.78;AVGPOST=0.6839;ERATE=0.0483;EUR_AF=0.76;LDAF=0.6591;RSQ=0.3693;SNPSOURCE=LOWCOV;THETA=0.0029;VT=SNP	GT:DS:PL	1|0:1.000:18,0,41
1	734491	rs7518433	T	C	100	PASS	AA=.;AC=1951;AF=0.89;AFR_AF=0.87;AMR_AF=0.92;AN=2184;ASN_AF=0.76;AVGPOST=0.9082;ERATE=0.0030;EUR_AF=0.99;LDAF=0.8637;RSQ=0.7381;SNPSOURCE=LOWCOV;THETA=0.0021;VT=SNP	GT:DS:PL	1|1:2.000:49,5,0
1	735682	rs138174321	G	C	100	PASS	AA=.;AC=78;AF=0.04;AFR_AF=0.01;AMR_AF=0.09;AN=2184;ASN_AF=0.0017;AVGPOST=0.9603;ERATE=0.0044;EUR_AF=0.05;LDAF=0.0523;RSQ=0.6771;SNPSOURCE=LOWCOV;THETA=0.0008;VT=SNP	GT:DS:PL	0|1:1.000:41,0,50
1	739210	rs141443091	A	G	100	PASS	AA=.;AC=1673;AF=0.77;AFR_AF=0.76;AMR_AF=0.73;AN=2184;ASN_AF=0.69;AVGPOST=0.8125;ERATE=0.0430;EUR_AF=0.85;LDAF=0.7242;RSQ=0.5967;SNPSOURCE=LOWCOV;THETA=0.0027;VT=SNP	GT:DS:PL	1|1:2.000:50,19,0
1	739426	rs3131973	A	G	100	PASS	AA=.;AC=2156;AF=0.99;AFR_AF=0.96;AMR_AF=0.99;AN=2184;ASN_AF=0.99;AVGPOST=0.9750;ERATE=0.0017;EUR_AF=1.00;LDAF=0.9781;RSQ=0.5788;SNPSOURCE=LOWCOV;THETA=0.0018;VT=SNP	GT:DS:PL	1|1:2.000:49,8,0
1	739528	rs3094317	G	A	100	PASS	AA=.;AC=1844;AF=0.84;AFR_AF=0.86;AMR_AF=0.84;AN=2184;ASN_AF=0.75;AVGPOST=0.9163;ERATE=0.0058;EUR_AF=0.90;LDAF=0.8211;RSQ=0.8049;SNPSOURCE=LOWCOV;THETA=0.0049;VT=SNP	GT:DS:PL	1|1:1.950:49,5,0
1	741579	rs61770168	T	C	100	PASS	AA=.;AC=1903;AF=0.87;AFR_AF=0.87;AMR_AF=0.90;AN=2184;ASN_AF=0.72;AVGPOST=0.8651;ERATE=0.0081;EUR_AF=0.97;LDAF=0.8339;RSQ=0.6782;SNPSOURCE=LOWCOV;THETA=0.0020;VT=SNP	GT:DS:PL	1|1:1.850:0,0,0
1	748878	rs143214544	G	T	100	PASS	AA=.;AC=1345;AF=0.62;AFR_AF=0.30;AMR_AF=0.67;AN=2184;ASN_AF=0.65;AVGPOST=0.8836;ERATE=0.0088;EUR_AF=0.77;LDAF=0.6043;RSQ=0.8266;SNPSOURCE=LOWCOV;THETA=0.0120;VT=SNP	GT:DS:PL	1|1:1.950:49,7,0
1	750013	rs12409695	C	T	100	PASS	AA=.;AC=1926;AF=0.88;AFR_AF=0.85;AMR_AF=0.88;AN=2184;ASN_AF=0.90;AVGPOST=0.7956;ERATE=0.0092;EUR_AF=0.89;LDAF=0.7929;RSQ=0.4429;SNPSOURCE=LOWCOV;THETA=0.0024;VT=SNP	GT:DS:PL	1|1:1.750:0,0,0
1	752566	rs3094315	G	A	100	PASS	AA=.;AC=1634;AF=0.75;AFR_AF=0.41;AMR_AF=0.82;AN=2184;ASN_AF=0.87;AVGPOST=0.9950;ERATE=0.0011;EUR_AF=0.84;LDAF=0.7489;RSQ=0.9908;SNPSOURCE=LOWCOV;THETA=0.0018;VT=SNP	GT:DS:PL	1|1:2.000:0,0,0
1	752721	rs3131972	A	G	100	PASS	AA=.;AC=1483;AF=0.68;AFR_AF=0.32;AMR_AF=0.74;AN=2184;ASN_AF=0.75;AVGPOST=0.9944;ERATE=0.0012;EUR_AF=0.83;LDAF=0.6786;RSQ=0.9911;SNPSOURCE=LOWCOV;THETA=0.0009;VT=SNP	GT:DS:PL	1|1:2.000:50,17,0
1	752894	rs3131971	T	C	100	PASS	AA=.;AC=1619;AF=0.74;AFR_AF=0.52;AMR_AF=0.79;AN=2184;ASN_AF=0.83;AVGPOST=0.9641;ERATE=0.0017;EUR_AF=0.80;LDAF=0.7375;RSQ=0.9323;SNPSOURCE=LOWCOV;THETA=0.0004;VT=SNP	GT:DS:PL	1|1:2.000:49,5,0
1	753405	rs61770173	C	A	100	PASS	AA=.;AC=1657;AF=0.76;AFR_AF=0.43;AMR_AF=0.83;AN=2184;ASN_AF=0.86;AVGPOST=0.8862;ERATE=0.0102;EUR_AF=0.86;LDAF=0.7201;RSQ=0.8043;SNPSOURCE=LOWCOV;THETA=0.0007;VT=SNP	GT:DS:PL	1|1:2.000:50,10,0
1	753474	rs2073814	C	G	100	PASS	AA=.;AC=1361;AF=0.62;AFR_AF=0.18;AMR_AF=0.70;AN=2184;ASN_AF=0.69;AVGPOST=0.9365;ERATE=0.0099;EUR_AF=0.83;LDAF=0.6117;RSQ=0.9133;SNPSOURCE=LOWCOV;THETA=0.0010;VT=SNP	GT:DS:PL	1|1:2.000:50,10,0
1	753849	rs58324164	G	T	100	PASS	AA=.;AC=267;AF=0.12;AFR_AF=0.03;AMR_AF=0.17;AN=2184;ASN_AF=0.12;AVGPOST=0.8303;ERATE=0.0018;EUR_AF=0.16;LDAF=0.1822;RSQ=0.6041;SNPSOURCE=LOWCOV;THETA=0.0048;VT=SNP	GT:DS:PL	1|1:1.100:0,0,0
1	754182	rs3131969	A	G	100	PASS	AA=.;AC=1513;AF=0.69;AFR_AF=0.37;AMR_AF=0.75;AN=2184;ASN_AF=0.70;AVGPOST=0.9910;ERATE=0.0006;EUR_AF=0.87;LDAF=0.6912;RSQ=0.9849;SNPSOURCE=LOWCOV;THETA=0.0003;VT=SNP	GT:DS:PL	1|1:2.000:49,8,0
1	754192	rs3131968	A	G	100	PASS	AA=.;AC=1511;AF=0.69;AFR_AF=0.37;AMR_AF=0.75;AN=2184;ASN_AF=0.70;AVGPOST=0.9900;ERATE=0.0006;EUR_AF=0.87;LDAF=0.6904;RSQ=0.9841;SNPSOURCE=LOWCOV;THETA=0.0017;VT=SNP	GT:DS:PL	1|1:2.000:49,6,0
1	754334	rs3131967	T	C	100	PASS	AA=.;AC=1492;AF=0.68;AFR_AF=0.37;AMR_AF=0.72;AN=2184;ASN_AF=0.72;AVGPOST=0.9855;ERATE=0.0010;EUR_AF=0.84;LDAF=0.6843;RSQ=0.9781;SNPSOURCE=LOWCOV;THETA=0.0018;VT=SNP	GT:DS:PL	1|1:2.000:50,14,0
1	754503	rs3115859	G	A	100	PASS	AA=.;AC=1503;AF=0.69;AFR_AF=0.36;AMR_AF=0.74;AN=2184;ASN_AF=0.75;AVGPOST=0.9952;ERATE=0.0008;EUR_AF=0.83;LDAF=0.6880;RSQ=0.9913;SNPSOURCE=LOWCOV;THETA=0.0009;VT=SNP	GT:DS:PL	1|1:2.000:49,8,0
1	754964	rs3131966	C	T	100	PASS	AA=.;AC=1451;AF=0.66;AFR_AF=0.36;AMR_AF=0.70;AN=2184;ASN_AF=0.72;AVGPOST=0.9822;ERATE=0.0009;EUR_AF=0.81;LDAF=0.6649;RSQ=0.9730;SNPSOURCE=LOWCOV;THETA=0.0012;VT=SNP	GT:DS:PL	1|1:2.000:50,13,0
1	755775	rs3131965	A	G	100	PASS	AA=.;AC=1554;AF=0.71;AFR_AF=0.44;AMR_AF=0.74;AN=2184;ASN_AF=0.82;AVGPOST=0.9192;ERATE=0.0159;EUR_AF=0.79;LDAF=0.6943;RSQ=0.8572;SNPSOURCE=LOWCOV;THETA=0.0007;VT=SNP	GT:DS:PL	1|1:2.000:49,8,0
1	755887	rs3131964	C	G	100	PASS	AA=.;AC=2152;AF=0.99;AFR_AF=0.95;AMR_AF=0.99;AN=2184;ASN_AF=1.00;AVGPOST=0.9961;ERATE=0.0006;EUR_AF=1.00;LDAF=0.9836;RSQ=0.9015;SNPSOURCE=LOWCOV;THETA=0.0008;VT=SNP	GT:DS:PL	1|1:2.000:46,6,0
1	755890	rs3115858	A	T	100	PASS	AA=.;AC=1666;AF=0.76;AFR_AF=0.46;AMR_AF=0.82;AN=2184;ASN_AF=0.86;AVGPOST=0.9779;ERATE=0.0007;EUR_AF=0.85;LDAF=0.7603;RSQ=0.9633;SNPSOURCE=LOWCOV;THETA=0.0003;VT=SNP	GT:DS:PL	1|1:2.000:31,3,0
1	756604	rs3131962	A	G	100	PASS	AA=.;AC=1628;AF=0.75;AFR_AF=0.46;AMR_AF=0.80;AN=2184;ASN_AF=0.84;AVGPOST=0.9568;ERATE=0.0104;EUR_AF=0.84;LDAF=0.7342;RSQ=0.9211;SNPSOURCE=LOWCOV;THETA=0.0016;VT=SNP	GT:DS:PL	1|1:2.000:50,16,0
1	757640	rs3115853	G	A	100	PASS	AA=.;AC=1439;AF=0.66;AFR_AF=0.23;AMR_AF=0.74;AN=2184;ASN_AF=0.70;AVGPOST=0.9944;ERATE=0.0006;EUR_AF=0.87;LDAF=0.6590;RSQ=0.9926;SNPSOURCE=LOWCOV;THETA=0.0009;VT=SNP	GT:DS:PL	1|1:2.000:50,28,0
1	757734	rs4951929	C	T	100	PASS	AA=.;AC=1685;AF=0.77;AFR_AF=0.46;AMR_AF=0.83;AN=2184;ASN_AF=0.87;AVGPOST=0.9983;ERATE=0.0004;EUR_AF=0.87;LDAF=0.7715;RSQ=0.9963;SNPSOURCE=LOWCOV;THETA=0.0011;VT=SNP	GT:DS:PL	1|1:2.000:50,17,0
1	757936	rs4951862	C	A	100	PASS	AA=.;AC=1684;AF=0.77;AFR_AF=0.46;AMR_AF=0.83;AN=2184;ASN_AF=0.87;AVGPOST=0.9955;ERATE=0.0004;EUR_AF=0.87;LDAF=0.7698;RSQ=0.9917;SNPSOURCE=LOWCOV;THETA=0.0005;VT=SNP	GT:DS:PL	1|1:2.000:50,11,0
1	758048	rs3131957	A	G	100	PASS	AA=.;AC=121;AF=0.06;AFR_AF=0.0020;AMR_AF=0.08;AN=2184;AVGPOST=0.9807;ERATE=0.0010;EUR_AF=0.12;LDAF=0.0621;RSQ=0.8729;SNPSOURCE=LOWCOV;THETA=0.0012;VT=SNP	GT:DS:PL	1|0:1.000:47,0,13
1	758144	rs3131956	A	G	100	PASS	AA=.;AC=1659;AF=0.76;AFR_AF=0.46;AMR_AF=0.82;AN=2184;ASN_AF=0.87;AVGPOST=0.9910;ERATE=0.0013;EUR_AF=0.84;LDAF=0.7592;RSQ=0.9835;SNPSOURCE=LOWCOV;THETA=0.0006;VT=SNP	GT:DS:PL	1|1:2.000:50,17,0

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

Input2: Father VCF files

##fileformat=VCFv4.1
##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	father
1	6522101	.	C	G	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=0.9547;SNPSOURCE=EXOME;THETA=0.0014;VT=SNP;936042258237	GT:DS:PL	0|1:1.000:50,0,50
1	11796321	rs1801133	G	A	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=0.9547;SNPSOURCE=EXOME;THETA=0.0014;VT=SNP;936042258237	GT:DS:PL	0|1:1.000:50,0,50
1	12091410	rs140706620	G	A	100	PASS	AA=G;AC=3;AF=0.0014;AN=2184;AVGPOST=1.0000;ERATE=0.0004;EUR_AF=0.0040;LDAF=0.0014;RSQ=0.9844;SNPSOURCE=LOWCOV,EXOME;THETA=0.0006;VT=SNP;0325217693434	GT:DS:PL	0|1:1.000:50,0,50
1	13368549	rs201258581	C	T	100	PASS	AA=.;AC=404;AF=0.18;AFR_AF=0.04;AMR_AF=0.28;AN=2184;ASN_AF=0.17;AVGPOST=0.7199;ERATE=0.0114;EUR_AF=0.24;LDAF=0.2816;RSQ=0.3941;SNPSOURCE=EXOME;THETA=0.0050;VT=SNP;0212025332681	GT:DS:PL	0|1:0.800:0,0,0
1	22203106	rs137904249	C	T	100	PASS	AA=C;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=0.9756;SNPSOURCE=LOWCOV;THETA=0.0002;VT=SNP;730321775122	GT:DS:PL	0|1:1.000:50,0,50
1	23845566	rs139052092	G	A	100	PASS	AA=G;AC=3;AF=0.0014;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0040;LDAF=0.0014;RSQ=0.9844;SNPSOURCE=EXOME;THETA=0.0028;VT=SNP;160.221212360292	GT:DS:PL	1|0:1.000:50,0,50
1	24083585	rs201983548	T	G	100	PASS	AA=T;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9999;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=0.9135;SNPSOURCE=EXOME;THETA=0.0004;VT=SNP;0517755763585	GT:DS:PL	0|1:1.000:50,0,50
1	26608852	rs61775089	G	A	100	PASS	AA=-;AC=600;AF=0.27;AFR_AF=0.29;AMR_AF=0.28;AN=2184;ASN_AF=0.17;AVGPOST=0.8275;ERATE=0.0545;EUR_AF=0.35;LDAF=0.3072;RSQ=0.5934;SNPSOURCE=LOWCOV;THETA=0.0002;VT=SNP;130444039285	GT:DS:PL	0|1:1.000:50,0,50
1	43296492	rs56047316	G	A	100	PASS	AA=G;AC=3;AF=0.0014;AMR_AF=0.0028;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0014;RSQ=0.9844;SNPSOURCE=LOWCOV,EXOME;THETA=0.0009;VT=SNP;177958457958	GT:DS:PL	1|0:1.000:50,0,50
1	45475906	rs182666370	G	A	100	PASS	AA=G;AC=7;AF=0.0032;AFR_AF=0.0020;AN=2184;ASN_AF=0.01;AVGPOST=0.9974;ERATE=0.0029;EUR_AF=0.0040;LDAF=0.0038;RSQ=0.7163;SNPSOURCE=LOWCOV,EXOME;THETA=0.0027;VT=SNP;0682685007233	GT:DS:PL	0|1:1.000:50,0,50
1	46977886	rs114486361	G	C	100	PASS	AA=G;AC=4;AF=0.0018;AN=2184;AVGPOST=0.9988;ERATE=0.0005;EUR_AF=0.01;LDAF=0.0024;RSQ=0.7924;SNPSOURCE=LOWCOV,EXOME;THETA=0.0002;VT=SNP;259457423477	GT:DS:PL	1|0:1.000:50,0,50
1	62560271	rs2131925	C	T	100	PASS	AA=C;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=1.0000;SNPSOURCE=EXOME;THETA=0.0007;VT=SNP;12420928946	GT:DS:PL	0|1:1.000:50,0,50
1	68949705	rs199589135	C	T	100	PASS	AA=C;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=1.0000;SNPSOURCE=EXOME;THETA=0.0007;VT=SNP;12420928946	GT:DS:PL	0|1:1.000:50,0,50
1	93101869	rs201080134	C	T	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0002;EUR_AF=0.0013;LDAF=0.0004;RSQ=0.9500;SNPSOURCE=EXOME;THETA=0.0006;VT=SNP;256034090873	GT:DS:PL	1|0:0.950:50,0,50
1	109793077	rs62623708	C	A	100	PASS	AA=N;AC=5;AF=0.0023;AN=2184;AVGPOST=0.9997;ERATE=0.0003;EUR_AF=0.01;LDAF=0.0024;RSQ=0.9432;SNPSOURCE=LOWCOV,EXOME;THETA=0.0030;VT=SNP;180436150653	GT:DS:PL	0|1:1.000:50,0,50
1	110230520	rs200184852	G	A	100	PASS	AA=G;AC=364;AF=0.17;AFR_AF=0.04;AMR_AF=0.15;AN=2184;ASN_AF=0.22;AVGPOST=0.8431;ERATE=0.0006;EUR_AF=0.22;LDAF=0.1872;RSQ=0.6532;SNPSOURCE=EXOME;THETA=0.0015;VT=SNP;0586366035612	GT:DS:PL	1|0:0.850:0,0,0
1	110282482	rs150988571	C	T	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9998;ERATE=0.0004;EUR_AF=0.0013;LDAF=0.0010;RSQ=0.8893;SNPSOURCE=LOWCOV;THETA=0.0005;VT=SNP;0968554072005	GT:DS:PL	0|1:1.000:50,0,50
1	118629525	rs146179421	G	C	100	PASS	AA=G;AC=3;AF=0.0014;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0040;LDAF=0.0014;RSQ=1.0000;SNPSOURCE=LOWCOV,EXOME;THETA=0.0007;VT=SNP;142839583257	GT:DS:PL	0|1:1.000:50,0,50
1	146461208	rs185738011	G	A	100	PASS	AA=N;AC=1038;AF=0.48;AFR_AF=0.51;AMR_AF=0.54;AN=2184;ASN_AF=0.38;AVGPOST=0.7264;ERATE=0.0084;EUR_AF=0.49;LDAF=0.4747;RSQ=0.5892;SNPSOURCE=LOWCOV;THETA=0.0033;VT=SNP;00223687405844	GT:DS:PL	0|1:0.800:0,0,0
1	146461219	rs189050702	C	T	100	PASS	AA=N;AC=1032;AF=0.47;AFR_AF=0.49;AMR_AF=0.53;AN=2184;ASN_AF=0.37;AVGPOST=0.7351;ERATE=0.0161;EUR_AF=0.51;LDAF=0.4858;RSQ=0.6045;SNPSOURCE=LOWCOV;THETA=0.0183;VT=SNP;00309483671738	GT:DS:PL	0|1:0.600:0,1,6
1	146672815	rs148940888	T	G	100	PASS	AA=.;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0004;RSQ=0.9500;SNPSOURCE=LOWCOV,EXOME;THETA=0.0007;VT=SNP;128423333438	GT:DS:PL	1|0:0.950:50,0,50
1	158906777	rs111499233	A	G	100	PASS	AA=A;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=0.9756;SNPSOURCE=LOWCOV,EXOME;THETA=0.0007;VT=SNP;178696341439	GT:DS:PL	0|1:0.950:50,0,50
1	182797925	rs185002399	G	A	100	PASS	AA=G;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=0.9547;SNPSOURCE=LOWCOV,EXOME;THETA=0.0012;VT=SNP;160.342273569509	GT:DS:PL	1|0:1.000:50,0,50
1	183481999	rs185963873	G	T	100	PASS	AA=G;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=0.9547;SNPSOURCE=LOWCOV,EXOME;THETA=0.0004;VT=SNP;0627603606502	GT:DS:PL	1|0:1.000:50,0,50
1	201294183	rs200484616	C	T	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=1.0000;SNPSOURCE=EXOME;THETA=0.0004;VT=SNP;304739020128	GT:DS:PL	1|0:1.000:50,0,50
1	202700068	rs34216958	C	T	100	PASS	AA=C;AC=3;AF=0.0014;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0040;LDAF=0.0019;RSQ=0.9882;SNPSOURCE=LOWCOV,EXOME;THETA=0.0005;VT=SNP;167540152082	GT:DS:PL	1|0:1.000:50,0,50
1	203681172	rs148318069	A	G	100	PASS	AA=A;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0004;RSQ=0.9500;SNPSOURCE=EXOME;THETA=0.0003;VT=SNP;160.131357809587	GT:DS:PL	0|1:0.950:50,0,50
1	210194555	rs145963511	C	T	100	PASS	AA=C;AC=2;AF=0.0009;AMR_AF=0.0028;AN=2184;AVGPOST=1.0000;ERATE=0.0005;EUR_AF=0.0013;LDAF=0.0009;RSQ=0.9756;SNPSOURCE=LOWCOV,EXOME;THETA=0.0002;VT=SNP;063945826042	GT:DS:PL	0|1:0.950:50,0,50
1	213414299	rs139942392	T	C	100	PASS	AA=T;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=0.9756;SNPSOURCE=LOWCOV,EXOME;THETA=0.0009;VT=SNP;083380793816	GT:DS:PL	0|1:1.000:50,0,50
1	220311332	rs143722284	G	A	100	PASS	AA=G;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=1.0000;SNPSOURCE=LOWCOV,EXOME;THETA=0.0005;VT=SNP;160.760687453369	GT:DS:PL	1|0:1.000:50,0,50
1	223986364	rs139578991	C	G	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9999;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=0.9049;SNPSOURCE=LOWCOV,EXOME;THETA=0.0004;VT=SNP;093133415351	GT:DS:PL	0|1:0.950:50,0,50
1	226173167	rs193190607	A	T	100	PASS	AA=A;AC=5;AF=0.0023;AMR_AF=0.01;AN=2184;AVGPOST=0.9999;ERATE=0.0006;EUR_AF=0.0040;LDAF=0.0023;RSQ=0.9813;SNPSOURCE=LOWCOV,EXOME;THETA=0.0008;VT=SNP;0920767216874	GT:DS:PL	1|0:1.000:50,0,50
1	228290663	rs181874649	G	C	100	PASS	AA=G;AC=452;AF=0.21;AFR_AF=0.22;AMR_AF=0.20;AN=2184;ASN_AF=0.24;AVGPOST=0.7321;ERATE=0.0537;EUR_AF=0.18;LDAF=0.2843;RSQ=0.3600;SNPSOURCE=LOWCOV;THETA=0.0010;VT=SNP;160.286496937309	GT:DS:PL	0|1:0.700:0,0,47
1	230928193	rs148405103	G	A	100	PASS	AA=G;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=1.0000;SNPSOURCE=LOWCOV,EXOME;THETA=0.0015;VT=SNP;471088393691	GT:DS:PL	0|1:1.000:50,0,50
1	233511776	rs34984140	C	T	100	PASS	AA=C;AC=8;AF=0.0037;AFR_AF=0.0020;AMR_AF=0.01;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.01;LDAF=0.0037;RSQ=1.0000;SNPSOURCE=LOWCOV,EXOME;THETA=0.0004;VT=SNP;311840588171	GT:DS:PL	0|1:1.000:50,0,50
1	247978544	rs113112592	G	A	100	PASS	AA=G;AC=386;AF=0.18;AFR_AF=0.01;AMR_AF=0.20;AN=2184;ASN_AF=0.29;AVGPOST=0.7801;ERATE=0.0062;EUR_AF=0.19;LDAF=0.2267;RSQ=0.5527;SNPSOURCE=EXOME;THETA=0.0007;VT=SNP;00446767063553	GT:DS:PL	1|0:0.650:0,1,9
1	248201930	rs185106511	C	T	100	PASS	AA=.;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0002;EUR_AF=0.0013;LDAF=0.0005;RSQ=1.0000;SNPSOURCE=LOWCOV,EXOME;THETA=0.0012;VT=SNP;105127243899	GT:DS:PL	0|1:1.000:50,0,50
2	25991689	rs147191545	T	C	100	PASS	AA=T;AC=3;AF=0.0014;AN=2184;AVGPOST=0.9998;ERATE=0.0003;EUR_AF=0.0040;LDAF=0.0015;RSQ=0.9298;SNPSOURCE=LOWCOV;THETA=0.0004;VT=SNP;05648489902	GT:DS:PL	1|0:1.000:50,0,50
2	27324354	rs1057391	C	T	100	PASS	AA=c;AC=46;AF=0.02;AFR_AF=0.01;AMR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.9474;ERATE=0.0099;EUR_AF=0.04;LDAF=0.0396;RSQ=0.4540;SNPSOURCE=LOWCOV;THETA=0.0019;VT=SNP;160.102274530818	GT:DS:PL	0|1:0.900:16,0,50
2	37268413	rs183316466	C	T	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9999;ERATE=0.0002;EUR_AF=0.0013;LDAF=0.0004;RSQ=0.8999;SNPSOURCE=LOWCOV,EXOME;THETA=0.0005;VT=SNP;109477131116	GT:DS:PL	1|0:0.900:50,0,50
2	46603764	rs150797491	T	A	100	PASS	AA=T;AC=2;AF=0.0009;AMR_AF=0.0028;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0009;RSQ=0.9768;SNPSOURCE=EXOME;THETA=0.0012;VT=SNP;160.444223886672	GT:DS:PL	1|0:1.000:50,0,50
2	48982755	rs188002889	G	A	100	PASS	AA=G;AC=140;AF=0.06;AFR_AF=0.10;AMR_AF=0.03;AN=2184;ASN_AF=0.01;AVGPOST=0.8934;ERATE=0.0122;EUR_AF=0.10;LDAF=0.0965;RSQ=0.5263;SNPSOURCE=LOWCOV;THETA=0.0002;VT=SNP;185202985566	GT:DS:PL	1|0:0.900:18,0,37
2	79385481	rs199992892	C	T	100	PASS	AA=C;AC=124;AF=0.06;AFR_AF=0.09;AMR_AF=0.08;AN=2184;ASN_AF=0.04;AVGPOST=0.9911;ERATE=0.0421;EUR_AF=0.04;LDAF=0.0571;RSQ=0.9370;SNPSOURCE=EXOME;THETA=0.0004;VT=SNP;0163310396696	GT:DS:PL	0|1:1.000:50,0,50
2	88409984	rs72845818	G	A	100	PASS	AA=G;AC=4;AF=0.0018;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.01;LDAF=0.0019;RSQ=0.9882;SNPSOURCE=LOWCOV,EXOME;THETA=0.0001;VT=SNP;488985731387	GT:DS:PL	1|0:1.000:50,0,50
2	95540540	rs76696553	C	T	100	PASS	AA=.;AC=408;AF=0.19;AFR_AF=0.17;AMR_AF=0.17;AN=2184;ASN_AF=0.22;AVGPOST=0.9050;ERATE=0.0849;EUR_AF=0.18;LDAF=0.2177;RSQ=0.7454;SNPSOURCE=EXOME;THETA=0.0020;VT=SNP;0137528395156	GT:DS:PL	1|0:0.950:20,0,42
2	96963419	rs142729495	T	C	100	PASS	AA=T;AC=5;AF=0.0023;AMR_AF=0.0028;AN=2184;AVGPOST=1.0000;ERATE=0.0002;EUR_AF=0.01;LDAF=0.0023;RSQ=1.0000;SNPSOURCE=LOWCOV,EXOME;THETA=0.0003;VT=SNP;0494163231842	GT:DS:PL	0|1:1.000:50,0,50
2	97482646	rs190607200	T	G	100	PASS	AA=T;AC=191;AF=0.09;AFR_AF=0.12;AMR_AF=0.04;AN=2184;ASN_AF=0.12;AVGPOST=0.7915;ERATE=0.0138;EUR_AF=0.06;LDAF=0.1562;RSQ=0.3634;SNPSOURCE=LOWCOV;THETA=0.0008;VT=SNP;160.877650509826	GT:DS:PL	0|1:0.700:0,0,0
2	113152295	rs200687738	C	G	100	PASS	AA=c;AC=1442;AF=0.66;AFR_AF=0.58;AMR_AF=0.67;AN=2184;ASN_AF=0.73;AVGPOST=0.6454;ERATE=0.0263;EUR_AF=0.66;LDAF=0.6121;RSQ=0.3558;SNPSOURCE=EXOME;THETA=0.0017;VT=SNP;0271043773265	GT:DS:PL	1|1:1.300:0,0,0
2	128408354	rs151091711	C	A	100	PASS	AA=c;AC=6;AF=0.0027;AMR_AF=0.0028;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.01;LDAF=0.0027;RSQ=1.0000;SNPSOURCE=LOWCOV,EXOME;THETA=0.0013;VT=SNP;131213211388	GT:DS:PL	1|0:1.000:50,0,50
2	131128829	rs144167090	G	C	100	PASS	AA=G;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=1.0000;SNPSOURCE=EXOME;THETA=0.0005;VT=SNP;0225676044077	GT:DS:PL	1|0:1.000:50,0,50
2	131279688	rs182508174	T	C	100	PASS	AA=.;AC=1182;AF=0.54;AFR_AF=0.43;AMR_AF=0.51;AN=2184;ASN_AF=0.62;AVGPOST=0.6206;ERATE=0.0075;EUR_AF=0.57;LDAF=0.5502;RSQ=0.3638;SNPSOURCE=LOWCOV;THETA=0.0003;VT=SNP;0639421690694	GT:DS:PL	1|1:1.450:0,0,0
2	133542559	rs188065336	C	T	100	PASS	AA=c;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9997;ERATE=0.0004;EUR_AF=0.0013;LDAF=0.0006;RSQ=0.7337;SNPSOURCE=LOWCOV,EXOME;THETA=0.0002;VT=SNP;0883572186547	GT:DS:PL	1|0:0.950:50,0,50
2	176945176	rs183677245	C	G	100	PASS	AA=C;AC=342;AF=0.16;AFR_AF=0.22;AMR_AF=0.15;AN=2184;ASN_AF=0.12;AVGPOST=0.7146;ERATE=0.0195;EUR_AF=0.15;LDAF=0.2338;RSQ=0.3356;SNPSOURCE=LOWCOV;THETA=0.0003;VT=SNP;160.446298843015	GT:DS:PL	0|1:1.150:0,0,0
2	187693393	rs142085122	G	C	100	PASS	AA=G;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9995;ERATE=0.0002;EUR_AF=0.0013;LDAF=0.0007;RSQ=0.7215;SNPSOURCE=LOWCOV,EXOME;THETA=0.0004;VT=SNP;0596031411015	GT:DS:PL	0|1:1.000:50,0,50
2	207834072	rs144914072	C	T	100	PASS	AA=C;AC=2;AF=0.0009;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0009;RSQ=0.9768;SNPSOURCE=EXOME;THETA=0.0005;VT=SNP;051439268844	GT:DS:PL	1|0:1.000:50,0,50
2	220040963	rs145875060	G	A	100	PASS	AA=G;AC=3;AF=0.0014;AMR_AF=0.0028;AN=2184;AVGPOST=0.9998;ERATE=0.0003;EUR_AF=0.0026;LDAF=0.0015;RSQ=0.9405;SNPSOURCE=LOWCOV,EXOME;THETA=0.0006;VT=SNP;0855376499618	GT:DS:PL	1|0:1.000:50,0,50
2	223553200	rs181021442	T	C	100	PASS	AA=T;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9999;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=0.8803;SNPSOURCE=LOWCOV,EXOME;THETA=0.0004;VT=SNP;116475855617	GT:DS:PL	1|0:1.000:50,0,50
2	227924322	rs202243658	C	T	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9995;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0006;RSQ=0.6727;SNPSOURCE=EXOME;THETA=0.0009;VT=SNP;160.92570021981	GT:DS:PL	1|0:0.900:50,0,50
2	239180006	rs141480763	T	C	100	PASS	AA=T;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0005;RSQ=1.0000;SNPSOURCE=EXOME;THETA=0.0004;VT=SNP;329838705194	GT:DS:PL	0|1:1.000:50,0,50
3	14106332	rs113667859	G	C	100	PASS	AA=g;AC=652;AF=0.30;AFR_AF=0.27;AMR_AF=0.30;AN=2184;ASN_AF=0.26;AVGPOST=0.8919;ERATE=0.0748;EUR_AF=0.34;LDAF=0.3205;RSQ=0.7268;SNPSOURCE=LOWCOV;THETA=0.0004;VT=SNP;0299966173887	GT:DS:PL	1|0:1.000:23,0,37
3	14724483	rs74842937	T	C	100	PASS	AA=T;AC=42;AF=0.02;AFR_AF=0.02;AMR_AF=0.02;AN=2184;ASN_AF=0.02;AVGPOST=0.9779;ERATE=0.0207;EUR_AF=0.02;LDAF=0.0267;RSQ=0.6865;SNPSOURCE=LOWCOV,EXOME;THETA=0.0004;VT=SNP;0706236446246	GT:DS:PL	0|1:1.000:50,0,50
3	19479731	rs138531032	G	A	100	PASS	AA=G;AC=3;AF=0.0014;AN=2184;AVGPOST=0.9996;ERATE=0.0003;EUR_AF=0.0040;LDAF=0.0016;RSQ=0.9331;SNPSOURCE=LOWCOV,EXOME;THETA=0.0005;VT=SNP;160.16304278436	GT:DS:PL	1|0:1.000:50,0,50
3	27763427	rs12715125	G	C	100	PASS	AA=G;AC=807;AF=0.37;AFR_AF=0.33;AMR_AF=0.41;AN=2184;ASN_AF=0.48;AVGPOST=0.7321;ERATE=0.0191;EUR_AF=0.29;LDAF=0.3873;RSQ=0.5188;SNPSOURCE=LOWCOV;THETA=0.0005;VT=SNP;160.321973565726	GT:DS:PL	0|1:1.100:0,0,0
3	33038800	.	A	G	100	PASS	AA=A;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9995;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0007;RSQ=0.7063;SNPSOURCE=EXOME;THETA=0.0001;VT=SNP;160.539214980715	GT:DS:PL	1|0:1.000:50,0,50
3	45877082	rs200504234	C	T	100	PASS	AA=C;AC=1;AF=0.0005;AN=2184;AVGPOST=1.0000;ERATE=0.0002;EUR_AF=0.0013;LDAF=0.0005;RSQ=1.0000;SNPSOURCE=EXOME;THETA=0.0004;VT=SNP;194828930112	GT:DS:PL	1|0:1.000:50,0,50
3	47277065	rs143906701	C	A	100	PASS	AA=c;AC=2;AF=0.0009;AN=2184;AVGPOST=0.9999;ERATE=0.0004;EUR_AF=0.0026;LDAF=0.0009;RSQ=0.9524;SNPSOURCE=LOWCOV,EXOME;THETA=0.0010;VT=SNP;0618327827925	GT:DS:PL	0|1:1.000:50,0,50
3	49836244	rs202217438	A	G	100	PASS	AA=A;AC=1;AF=0.0005;AN=2184;AVGPOST=0.9995;ERATE=0.0003;EUR_AF=0.0013;LDAF=0.0007;RSQ=0.6996;SNPSOURCE=EXOME;THETA=0.0004;VT=SNP;134678142558	GT:DS:PL	0|1:1.000:50,0,50
3	75787372	rs142560684	A	T	100	PASS	AA=.;AC=453;AF=0.21;AFR_AF=0.15;AMR_AF=0.22;AN=2184;ASN_AF=0.22;AVGPOST=0.7675;ERATE=0.0064;EUR_AF=0.23;LDAF=0.2570;RSQ=0.5418;SNPSOURCE=LOWCOV;THETA=0.0031;VT=SNP;00852845492273	GT:DS:PL	1|0:1.050:0,0,0
3	75790513	rs149568659	T	C	100	PASS	AA=.;AC=1267;AF=0.58;AFR_AF=0.38;AMR_AF=0.65;AN=2184;ASN_AF=0.63;AVGPOST=0.7343;ERATE=0.0095;EUR_AF=0.64;LDAF=0.5230;RSQ=0.6569;SNPSOURCE=LOWCOV;THETA=0.0135;VT=SNP;00643804168803	GT:DS:PL	1|1:1.500:0,0,0
3	88108540	rs67376749	C	T	100	PASS	AA=C;AC=669;AF=0.31;AFR_AF=0.30;AMR_AF=0.26;AN=2184;ASN_AF=0.32;AVGPOST=0.8394;ERATE=0.1164;EUR_AF=0.33;LDAF=0.3543;RSQ=0.5587;SNPSOURCE=LOWCOV;THETA=0.0011;VT=SNP;170983987535	GT:DS:PL	0|1:0.850:10,0,50

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

Both examples files are 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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