#!/usr/bin/perl;
use strict; use v5.8.8;
use Data::Dumper;

##List all .var files in directory

my $path = '.'; #Reads same directory as running .pl file
opendir(DIR, $path);
my @files = grep { /\.var$/ } readdir(DIR); #Reads names of .var files into @files
@files = sort @files;
my @samples;
foreach (@files) {
	if ($_ =~ /\_/) {
		$_ =~ /(^.+?)\_/;
		push @samples, $1; 
	} else {
		$_ =~ /(^.+)\.var/;
		push @samples, $1;
	}
}
closedir(DIR);
@files = sort @files; 
my $file_count = @files;
print "\nRunning on $file_count files:\n";
print "@files ";

#Make unique list of variants observed in all opened .var files

my @variants; ##Create concatenated list of all variant locations and alleles
my @zygosity;
my $zyg;
my %zygos;
foreach my $file (@files) {
	open VAR, $file;
	chomp (my @var = <VAR>);
	##sub in $file for ID (3rd column)
	while ($var[0] =~ s/ID/$file/) {
		shift @var;
	}
	foreach (@var) {
		my @fields = split /\t/, $_;
		$fields[2] = $file;
		my $locus = join "\t", @fields[0,1,2,3,4,5];
		push @variants, $locus;
		#pull out genotype
		$fields[9] =~ /(^\d\/\d\:)/;
			if ($1 =~ /0\/1\:/) {
			$zyg = "HET"; } else { $zyg = "HOM"; }		
			$fields[9] = $zyg;
			# push @zygosity, $zyg;
			push @{$zygos{$locus}}, $zyg;
			}
	}
	close VAR;


my %variants_hash = map { $_, 1 } @variants; ##Generates the unique list
my @variants_list = keys %variants_hash;
%variants_hash = undef;
@variants_list = sort @variants_list; #List of just loci
my %variants_geno; #List of loci to which genotypes will be appended
my %variants_info; # List of variant information to append after genotypes for printing.

my $sum_variants = @variants_list;
print "\nRunning on $sum_variants non-redundant variants.\n";

# Pull out genotypes for all of the non-redundant variants for each individual

my @variant_geno; #Pointless array for anonymous assignation of arrays in hash

foreach my $file (@files) {
	open VAR, $file;
	my @var = <VAR>;	
	foreach my $variant (@variants_list) {
		my $found = 0;
		my $genotype = 'REF?';
		foreach my $line (@var) {	
			my @fields2 = split /\t/, $line;
				$fields2[2] = $file;
				$fields2[9] = $zygos{$variant};
				my $newline = join "\t", @fields2[0..123];
				$line = $newline;				
					if ($line =~ /$variant/) {
						if ($found == 0) {
					$variants_info{$variant} = (join "\t", @fields2[10..123]);
					$found ++;
				}
						if ($fields2[9] eq 'HET') {
					$genotype = 'HET';
				}
						if ($fields2[9] eq 'HOM') {
					$genotype = 'HOM';
				}
				last;	
				}}
			
		if ($variants_geno{$variant} =~ /./) {
			push @{$variants_geno{$variant}}, $genotype;
		} else {
			@{$variants_geno{$variant}} = [@variant_geno];
			push @{$variants_geno{$variant}}, $genotype;
		
	}}
	close VAR;
}

open OUT, ">$ARGV[0]" . 'merged.vars';

my $samples_list = join "\t", @samples;
print OUT "CHROM	POS	ID	REF	ALT	QUAL	$samples_list	Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	ExonicFunc.refGene	AAChange.refGene	Func.knownGene	Gene.knownGene	GeneDetail.knownGene	ExonicFunc.knownGene	AAChange.knownGene	avsnp144	1000g2015aug_all	1000g2015aug_afr	1000g2015aug_amr	1000g2015aug_sas	1000g2015aug_eur	1000g2015aug_eas	esp6500siv2_all	esp6500siv2_ea	esp6500siv2_aa	ExAC_ALL	ExAC_AFR	ExAC_AMR	ExAC_EAS	ExAC_FIN	ExAC_NFE	ExAC_OTH	ExAC_SAS	cosmic70	SIFT_score	SIFT_pred	Polyphen2_HDIV_score	Polyphen2_HDIV_pred	Polyphen2_HVAR_score	Polyphen2_HVAR_pred	LRT_score	LRT_pred	MutationTaster_score	MutationTaster_pred	MutationAssessor_score	MutationAssessor_pred	FATHMM_score	FATHMM_pred	PROVEAN_score	PROVEAN_pred	VEST3_score	CADD_raw	CADD_phred	DANN_score	fathmm-MKL_coding_score	fathmm-MKL_coding_pred	MetaSVM_score	MetaSVM_pred	MetaLR_score	MetaLR_pred	integrated_fitCons_score	integrated_confidence_value	GERP++_RS	phyloP7way_vertebrate	phyloP20way_mammalian	phastCons7way_vertebrate	phastCons20way_mammalian	SiPhy_29way_logOdds	Interpro_domain	dbscSNV_ADA_SCORE	dbscSNV_RF_SCORE	CLINSIG	CLNDBN	CLNACC	CLNDSDB	CLNDSDBID	HRC_AF	HRC_AC	HRC_AN	HRC_non1000G_AF	HRC_non1000G_AC	HRC_non1000G_AN	Kaviar_AF	Kaviar_AC	Kaviar_AN	nci60	KEY3	INFO_AC	INFO_AF	INFO_BaseQRankSum	INFO_ClippingRankSum	INFO_DP	INFO_DS	INFO_END	INFO_ExcessHet	INFO_FS	INFO_HaplotypeScore	INFO_InbreedingCoeff	INFO_MLEAC	INFO_MLEAF	INFO_MQ	INFO_MQRankSum	INFO_QD	INFO_RAW_MQ	INFO_ReadPosRankSum	INFO_SOR	seq	seq_flag	AAchange	Grantham	Mutability	FuentesFalsePositive	ACMG";


foreach my $variant_ident (@variants_list) {
	shift @{$variants_geno{$variant_ident}};
	my $genotypes = join "\t", @{$variants_geno{$variant_ident}};
	my $joined = join "\t", $variant_ident, $genotypes, $variants_info{$variant_ident};
	$joined =~ s/^\s+//;
	chop $joined;
	print OUT "$joined";
}

close OUT;

##</code><code>##

--Dummydata1.var--
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	IFS003-W	Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	ExonicFunc.refGene	AAChange.refGene	Func.knownGene	Gene.knownGene	GeneDetail.knownGene	ExonicFunc.knownGene	AAChange.knownGene	avsnp144	1000g2015aug_all	1000g2015aug_afr	1000g2015aug_amr	1000g2015aug_sas	1000g2015aug_eur	1000g2015aug_eas	esp6500siv2_all	esp6500siv2_ea	esp6500siv2_aa	ExAC_ALL	ExAC_AFR	ExAC_AMR	ExAC_EAS	ExAC_FIN	ExAC_NFE	ExAC_OTH	ExAC_SAS	cosmic70	SIFT_score	SIFT_pred	Polyphen2_HDIV_score	Polyphen2_HDIV_pred	Polyphen2_HVAR_score	Polyphen2_HVAR_pred	LRT_score	LRT_pred	MutationTaster_score	MutationTaster_pred	MutationAssessor_score	MutationAssessor_pred	FATHMM_score	FATHMM_pred	PROVEAN_score	PROVEAN_pred	VEST3_score	CADD_raw	CADD_phred	DANN_score	fathmm-MKL_coding_score	fathmm-MKL_coding_pred	MetaSVM_score	MetaSVM_pred	MetaLR_score	MetaLR_pred	integrated_fitCons_score	integrated_confidence_value	GERP++_RS	phyloP7way_vertebrate	phyloP20way_mammalian	phastCons7way_vertebrate	phastCons20way_mammalian	SiPhy_29way_logOdds	Interpro_domain	dbscSNV_ADA_SCORE	dbscSNV_RF_SCORE	CLINSIG	CLNDBN	CLNACC	CLNDSDB	CLNDSDBID	HRC_AF	HRC_AC	HRC_AN	HRC_non1000G_AF	HRC_non1000G_AC	HRC_non1000G_AN	Kaviar_AF	Kaviar_AC	Kaviar_AN	nci60	KEY3	INFO_AC	INFO_AF	INFO_BaseQRankSum	INFO_ClippingRankSum	INFO_DP	INFO_DS	INFO_END	INFO_ExcessHet	INFO_FS	INFO_HaplotypeScore	INFO_InbreedingCoeff	INFO_MLEAC	INFO_MLEAF	INFO_MQ	INFO_MQRankSum	INFO_QD	INFO_RAW_MQ	INFO_ReadPosRankSum	INFO_SOR	seq	seq_flag	AAchange	Grantham	Mutability	FuentesFalsePositive	ACMG
chr1	14653	.	C	T	191.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=0.00;DP=26;ExcessHet=3.0103;FS=6.641;MLEAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=0.580;QD=7.38;ReadPosRankSum=-1.830e-01;SOR=2.280	GT:AD:DP:GQ:PL	0/1:15,11:26:99:220,0,292	chr1	14653	14653	C	T	ncRNA_exonic	WASH7P				intergenic	NONE,MIR6859-3	dist=NONE;dist=2716			rs62635297																																																																			0.0011526	30	26028		chr1:14653:14653:C:T	1	0.5	1.23	0	26	no_DS	no_END	3.0103	6.641	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	32.19	0.58	7.38	no_RAW_MQ	-1.83E-01	2.28	AAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAA[C]GGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATT	pass	XX	.	0	1	0
chr1	16949	.	A	C	240.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.57;ClippingRankSum=0.00;DP=39;ExcessHet=3.0103;FS=1.264;MLEAC=1;MLEAF=0.500;MQ=21.03;MQRankSum=-7.380e-01;QD=6.17;ReadPosRankSum=1.62;SOR=0.693	GT:AD:DP:GQ:PL	0/1:24,15:39:99:269,0,502	chr1	16949	16949	A	C	ncRNA_exonic	WASH7P				downstream	MIR6859-3				rs199745162	0.0139776	0.0227	0.0144	0.0143	0.0159																																																														0.0159444	415	26028		chr1:16949:16949:A:C	1	0.5	1.57	0	39	no_DS	no_END	3.0103	1.264	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	21.03	-7.38E-01	6.17	no_RAW_MQ	1.62	0.693	CTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCA[A]TGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGA	pass	XX	.	0	1	0
chr1	17020	.	G	A	58.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.670e-01;ClippingRankSum=0.00;DP=43;ExcessHet=3.0103;FS=23.602;MLEAC=1;MLEAF=0.500;MQ=21.00;MQRankSum=0.00;QD=1.37;ReadPosRankSum=-1.126e+00;SOR=1.132	GT:AD:DP:GQ:PL	0/1:34,9:43:87:87,0,789	chr1	17020	17020	G	A	ncRNA_exonic	WASH7P				downstream	MIR6859-3				rs199740902																																																																			0.0141002	367	26028		chr1:17020:17020:G:A	1	0.5	-4.67E-01	0	43	no_DS	no_END	3.0103	23.602	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	21	0	1.37	no_RAW_MQ	-1.13E+00	1.132	ATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG[G]CCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCA	pass	XX	.	0	1	0
chr1	17385	.	G	A	81.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.653;ClippingRankSum=0.00;DP=71;ExcessHet=3.0103;FS=3.091;MLEAC=1;MLEAF=0.500;MQ=48.65;MQRankSum=0.417;QD=1.15;ReadPosRankSum=1.02;SOR=0.311	GT:AD:DP:GQ:PL	0/1:60,11:71:99:110,0,1715	chr1	17385	17385	G	A	ncRNA_exonic;splicing	MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4;WASH7P	NR_024540:exon6:c.588-17C>T			ncRNA_exonic	MIR6859-3				rs201535981										0.2454	0.2331	0.2857	0.0423	0.2817	0.2743	0.2321	0.2092																																																		0.0015912	246	154602		chr1:17385:17385:G:A	1	0.5	0.653	0	71	no_DS	no_END	3.0103	3.091	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	48.65	0.417	1.15	no_RAW_MQ	1.02	0.311	AGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATG[G]GGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCAC	pass	XX	.	0	0	0
chr1	17408	.	C	G	134.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.480e-01;ClippingRankSum=0.00;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.27;MQRankSum=-8.570e-01;QD=1.45;ReadPosRankSum=0.359;SOR=0.527	GT:AD:DP:GQ:PL	0/1:79,14:93:99:163,0,2339	chr1	17408	17408	C	G	ncRNA_exonic	MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4				ncRNA_exonic	MIR6859-3				rs747093451										0.0352	0.0339	0.049	0	0.0273	0.0438	0	0.0074																																																		0.0013842	214	154602		chr1:17408:17408:C:G	1	0.5	-9.48E-01	0	94	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	52.27	-8.57E-01	1.45	no_RAW_MQ	0.359	0.527	ACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCG[C]TGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCAC	pass	XX	.	0	0	0
chr1	17697	.	G	C	125.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.529e+00;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.25;MQRankSum=-8.310e-01;QD=4.49;ReadPosRankSum=1.07;SOR=0.124	GT:AD:DP:GQ:PL	0/1:21,7:28:99:154,0,714	chr1	17697	17697	G	C	ncRNA_exonic	WASH7P				upstream	MIR6859-3				rs374995955																																																																			0.0155602	405	26028		chr1:17697:17697:G:C	1	0.5	-2.53E+00	0	28	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	39.25	-8.31E-01	4.49	no_RAW_MQ	1.07	0.124	GCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGG[G]CTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAG	pass	XX	.	0	1	0

##</code><code>##

--Dummydata2.var--
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	IFS001_W1515808	Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	ExonicFunc.refGene	AAChange.refGene	Func.knownGene	Gene.knownGene	GeneDetail.knownGene	ExonicFunc.knownGene	AAChange.knownGene	avsnp144	1000g2015aug_all	1000g2015aug_afr	1000g2015aug_amr	1000g2015aug_sas	1000g2015aug_eur	1000g2015aug_eas	esp6500siv2_all	esp6500siv2_ea	esp6500siv2_aa	ExAC_ALL	ExAC_AFR	ExAC_AMR	ExAC_EAS	ExAC_FIN	ExAC_NFE	ExAC_OTH	ExAC_SAS	cosmic70	SIFT_score	SIFT_pred	Polyphen2_HDIV_score	Polyphen2_HDIV_pred	Polyphen2_HVAR_score	Polyphen2_HVAR_pred	LRT_score	LRT_pred	MutationTaster_score	MutationTaster_pred	MutationAssessor_score	MutationAssessor_pred	FATHMM_score	FATHMM_pred	PROVEAN_score	PROVEAN_pred	VEST3_score	CADD_raw	CADD_phred	DANN_score	fathmm-MKL_coding_score	fathmm-MKL_coding_pred	MetaSVM_score	MetaSVM_pred	MetaLR_score	MetaLR_pred	integrated_fitCons_score	integrated_confidence_value	GERP++_RS	phyloP7way_vertebrate	phyloP20way_mammalian	phastCons7way_vertebrate	phastCons20way_mammalian	SiPhy_29way_logOdds	Interpro_domain	dbscSNV_ADA_SCORE	dbscSNV_RF_SCORE	CLINSIG	CLNDBN	CLNACC	CLNDSDB	CLNDSDBID	HRC_AF	HRC_AC	HRC_AN	HRC_non1000G_AF	HRC_non1000G_AC	HRC_non1000G_AN	Kaviar_AF	Kaviar_AC	Kaviar_AN	nci60	KEY3	INFO_AC	INFO_AF	INFO_BaseQRankSum	INFO_ClippingRankSum	INFO_DP	INFO_DS	INFO_END	INFO_ExcessHet	INFO_FS	INFO_HaplotypeScore	INFO_InbreedingCoeff	INFO_MLEAC	INFO_MLEAF	INFO_MQ	INFO_MQRankSum	INFO_QD	INFO_RAW_MQ	INFO_ReadPosRankSum	INFO_SOR	seq	seq_flag	AAchange	Grantham	Mutability	FuentesFalsePositive	ACMG
chr1	14464	.	A	T	39.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.00;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=40.51;MQRankSum=-6.740e-01;QD=9.94;ReadPosRankSum=0.674;SOR=2.303	GT:AD:DP:GQ:PL	0/1:2,2:4:64:68,0,64	chr1	14464	14464	A	T	ncRNA_exonic	WASH7P				intergenic	NONE,MIR6859-3	dist=NONE;dist=2905			rs546169444	0.0958466	0.0144	0.1138	0.1943	0.1859	0.005																																																													0.0346166	901	26028		chr1:14464:14464:A:T	1	0.5	1.38	0	4	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	40.51	-6.74E-01	9.94	no_RAW_MQ	0.674	2.303	GTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACAC[A]GTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGA	pass	XX	.	0	1	0
chr1	17407	.	G	A	140.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.44;ClippingRankSum=0.00;DP=60;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.25;MQRankSum=1.74;QD=2.39;ReadPosRankSum=-1.500e-02;SOR=0.608	GT:AD:DP:GQ:PL	0/1:49,10:59:99:169,0,1261	chr1	17407	17407	G	A	ncRNA_exonic	MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4				ncRNA_exonic	MIR6859-3				rs372841554										0.0765	0.0303	0.054	0.0672	0.0273	0.0894	0.0714	0.1352																																																		0.0030013	464	154602		chr1:17407:17407:G:A	1	0.5	2.44	0	60	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	49.25	1.74	2.39	no_RAW_MQ	-1.50E-02	0.608	TACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCC[G]CTGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCA	pass	XX	.	0	0	0
chr1	17758	.	T	A	75.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;ClippingRankSum=0.00;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=38.87;MQRankSum=-5.240e-01;QD=15.15;ReadPosRankSum=-5.240e-01;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:63:104,0,63	chr1	17758	17758	T	A	ncRNA_splicing	WASH7P	NR_024540:exon5:c.451-16A>T			upstream	MIR6859-3																																																																											chr1:17758:17758:T:A	1	0.5	0.674	0	5	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	38.87	-5.24E-01	15.15	no_RAW_MQ	-5.24E-01	1.022	GTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAGAGGGCCAGGA[T]GGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGCTGCCATCCC	pass	XX	.	0	1	0
chr1	69511	.	A	G	2186.77	.	AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.68;QD=28.04;SOR=0.744	GT:AD:DP:GQ:PL	1/1:0,78:78:99:2215,234,0	chr1	69511	69511	A	G	exonic	OR4F5		nonsynonymous SNV	OR4F5:NM_001005484:exon1:c.A421G:p.T141A	exonic	OR4F5		nonsynonymous SNV	OR4F5:uc001aal.1:exon1:c.A421G:p.T141A	rs2691305							0.7598	0.8874	0.5441	0.9394	0.5942	0.9507	0.9994	0.9907	0.9716	0.9597	0.9832		0.652	T	0	B	0	B	0	N	1	P	-1.295	N	1.26	T	1.54	N	0.012	-0.784	0.047	0.454	0.003	N	-0.997	T	0	T	0.487	0	1.15	-0.016	-0.132	0.055	0.765	4.198	GPCR, rhodopsin-like, 7TM														0.54161	83734	154602	0.51	chr1:69511:69511:A:G	2	1	no_BaseQRankSum	no_ClippingRankSum	78	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	2	1	43.68	no_MQRankSum	28.04	no_RAW_MQ	no_ReadPosRankSum	0.744	ACTACACTACAATTATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTC[A]CATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCGTTTGCCGTG	pass	TA	.	0	1	0
chr1	138041	.	G	A	119.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.97;ClippingRankSum=0.00;DP=19;ExcessHet=3.0103;FS=8.903;MLEAC=1;MLEAF=0.500;MQ=30.73;MQRankSum=-1.007e+00;QD=6.30;ReadPosRankSum=1.18;SOR=0.493	GT:AD:DP:GQ:PL	0/1:12,7:19:99:148,0,289	chr1	138041	138041	G	A	ncRNA_exonic	LOC729737				intergenic	RP11-34P13.7,RP11-34P13.14	dist=4318;dist=1749			rs560358882	0.00239617		0.0029	0.0051	0.005																																																														0.0015368	40	26028		chr1:138041:138041:G:A	1	0.5	1.97	0	19	no_DS	no_END	3.0103	8.903	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	30.73	-1.01E+00	6.3	no_RAW_MQ	1.18	0.493	GAAGGGAAAAACTGGGCCTGGAAAGGCCGTTGTCAGGAATGAGCCCCATG[G]GCCTGAAGAGGCCACTGGCAGGCGGGAGCTGGGCCTGCCGAAGCGGCCGA	pass	XX	.	0	0	0
chr1	138156	.	G	T	120.84	.	AC=2;AF=1.00;AN=2;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=20.17;QD=20.14;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,6:6:18:149,18,0	chr1	138156	138156	G	T	ncRNA_exonic	LOC729737				intergenic	RP11-34P13.7,RP11-34P13.14	dist=4433;dist=1634			rs370691115																																																																			0.0967804	2519	26028		chr1:138156:138156:G:T	2	1	no_BaseQRankSum	no_ClippingRankSum	6	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	2	1	20.17	no_MQRankSum	20.14	no_RAW_MQ	no_ReadPosRankSum	0.693	GGACTCGGGAGGCCGCAGTGAAGCAACAGCTAGCTGGGCGTGGAGAGTCC[G]CTGTGAGGCAGAGGCTGGGCCTGTGCAGGCCTTCGGGAGGCAGGAGGCTG	pass	XX	.	0	0	0
chr1	139213	.	A	G	1774.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.140e+00;ClippingRankSum=0.00;DP=97;ExcessHet=3.0103;FS=3.809;MLEAC=1;MLEAF=0.500;MQ=39.41;MQRankSum=-1.653e+00;QD=18.30;ReadPosRankSum=-7.760e-01;SOR=1.060	GT:AD:DP:GQ:PGT:PID:PL	0/1:51,46:97:99:0|1:139213_A_G:1803,0,3192	chr1	139213	139213	A	G	ncRNA_exonic	LOC729737				downstream	RP11-34P13.14				rs370723703										0.2506	0.3787	0.2879	0.3404	0.25	0.2597	0.3083	0.2352																																																		0.0259699	4015	154602		chr1:139213:139213:A:G	1	0.5	-4.14E+00	0	97	no_DS	no_END	3.0103	3.809	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	39.41	-1.65E+00	18.3	no_RAW_MQ	-7.76E-01	1.06	GGAAGGTTGCCATGAGACAAAAGTTGGGCCTGGAAAGGCCCTTGTGAAGC[A]TGAGCTTGGCCTAAAGAGGCCACTGGGTGGCAGGAGCTGGGTGTGTAGAA	pass	XX	.	0	0	0
chr1	139233	.	C	A	1883.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.990e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=2.463;MLEAC=1;MLEAF=0.500;MQ=39.80;MQRankSum=0.636;QD=17.13;ReadPosRankSum=-1.834e+00;SOR=0.595	GT:AD:DP:GQ:PGT:PID:PL	0/1:56,54:110:99:0|1:139213_A_G:1912,0,3261	chr1	139233	139233	C	A	ncRNA_exonic	LOC729737				downstream	RP11-34P13.14				rs373847457										0.2478	0.3763	0.2985	0.3548	.	0.2577	0.3103	0.2308																																																		0.0254654	3937	154602		chr1:139233:139233:C:A	1	0.5	-9.99E-01	0	110	no_DS	no_END	3.0103	2.463	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	39.8	0.636	17.13	no_RAW_MQ	-1.83E+00	0.595	AAGTTGGGCCTGGAAAGGCCCTTGTGAAGCATGAGCTTGGCCTAAAGAGG[C]CACTGGGTGGCAGGAGCTGGGTGTGTAGAAGCTGCTGAAAGGTTGGGAGC	pass	XX	.	0	0	0

##</code><code>##

--Dummydata3.var--
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	IFS002_W1600378	Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	ExonicFunc.refGene	AAChange.refGene	Func.knownGene	Gene.knownGene	GeneDetail.knownGene	ExonicFunc.knownGene	AAChange.knownGene	avsnp144	1000g2015aug_all	1000g2015aug_afr	1000g2015aug_amr	1000g2015aug_sas	1000g2015aug_eur	1000g2015aug_eas	esp6500siv2_all	esp6500siv2_ea	esp6500siv2_aa	ExAC_ALL	ExAC_AFR	ExAC_AMR	ExAC_EAS	ExAC_FIN	ExAC_NFE	ExAC_OTH	ExAC_SAS	cosmic70	SIFT_score	SIFT_pred	Polyphen2_HDIV_score	Polyphen2_HDIV_pred	Polyphen2_HVAR_score	Polyphen2_HVAR_pred	LRT_score	LRT_pred	MutationTaster_score	MutationTaster_pred	MutationAssessor_score	MutationAssessor_pred	FATHMM_score	FATHMM_pred	PROVEAN_score	PROVEAN_pred	VEST3_score	CADD_raw	CADD_phred	DANN_score	fathmm-MKL_coding_score	fathmm-MKL_coding_pred	MetaSVM_score	MetaSVM_pred	MetaLR_score	MetaLR_pred	integrated_fitCons_score	integrated_confidence_value	GERP++_RS	phyloP7way_vertebrate	phyloP20way_mammalian	phastCons7way_vertebrate	phastCons20way_mammalian	SiPhy_29way_logOdds	Interpro_domain	dbscSNV_ADA_SCORE	dbscSNV_RF_SCORE	CLINSIG	CLNDBN	CLNACC	CLNDSDB	CLNDSDBID	HRC_AF	HRC_AC	HRC_AN	HRC_non1000G_AF	HRC_non1000G_AC	HRC_non1000G_AN	Kaviar_AF	Kaviar_AC	Kaviar_AN	nci60	KEY3	INFO_AC	INFO_AF	INFO_BaseQRankSum	INFO_ClippingRankSum	INFO_DP	INFO_DS	INFO_END	INFO_ExcessHet	INFO_FS	INFO_HaplotypeScore	INFO_InbreedingCoeff	INFO_MLEAC	INFO_MLEAF	INFO_MQ	INFO_MQRankSum	INFO_QD	INFO_RAW_MQ	INFO_ReadPosRankSum	INFO_SOR	seq	seq_flag	AAchange	Grantham	Mutability	FuentesFalsePositive	ACMG
chr1	14590	.	G	A	118.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.43;ClippingRankSum=0.00;DP=11;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=28.67;MQRankSum=-1.513e+00;QD=10.80;ReadPosRankSum=0.357;SOR=1.981	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,4:11:99:0|1:14590_G_A:147,0,307	chr1	14590	14590	G	A	ncRNA_exonic	WASH7P				intergenic	NONE,MIR6859-3	dist=NONE;dist=2779																																																																										chr1:14590:14590:G:A	1	0.5	2.43	0	11	no_DS	no_END	3.0103	3.09	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	28.67	-1.51E+00	10.8	no_RAW_MQ	0.357	1.981	CAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCC[G]TCACCCCCTCCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCC	pass	XX	.	0	1	0
chr1	14599	.	T	A	115.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=2.881;MLEAC=1;MLEAF=0.500;MQ=30.13;MQRankSum=-1.712e+00;QD=9.65;ReadPosRankSum=1.16;SOR=1.721	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,4:12:99:0|1:14590_G_A:144,0,349	chr1	14599	14599	T	A	ncRNA_exonic	WASH7P				intergenic	NONE,MIR6859-3	dist=NONE;dist=2770			rs531646671	0.147564	0.121	0.1758	0.2096	0.161	0.0893																																																													0.0283925	739	26028		chr1:14599:14599:T:A	1	0.5	0.253	0	12	no_DS	no_END	3.0103	2.881	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	30.13	-1.71E+00	9.65	no_RAW_MQ	1.16	1.721	CTTCCGCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCC[T]CCCAAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAG	homopolymer	XX	.	0	1	0
chr1	14604	.	A	G	151.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.02;ClippingRankSum=0.00;DP=12;ExcessHet=3.0103;FS=2.881;MLEAC=1;MLEAF=0.500;MQ=30.13;MQRankSum=-1.712e+00;QD=12.65;ReadPosRankSum=1.34;SOR=1.721	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,4:12:99:0|1:14590_G_A:180,0,346	chr1	14604	14604	A	G	ncRNA_exonic	WASH7P				intergenic	NONE,MIR6859-3	dist=NONE;dist=2765			rs541940975	0.147564	0.121	0.1758	0.2096	0.161	0.0893																																																													0.0285846	744	26028		chr1:14604:14604:A:G	1	0.5	1.02	0	12	no_DS	no_END	3.0103	2.881	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	30.13	-1.71E+00	12.65	no_RAW_MQ	1.34	1.721	GCTCCTTGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCA[A]GGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACG	pass	XX	.	0	1	0
chr1	14610	.	T	C	151.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.16;ClippingRankSum=0.00;DP=13;ExcessHet=3.0103;FS=3.123;MLEAC=1;MLEAF=0.500;MQ=31.00;MQRankSum=-1.442e+00;QD=11.67;ReadPosRankSum=0.860;SOR=2.030	GT:AD:DP:GQ:PGT:PID:PL	0/1:8,5:13:99:0|1:14590_G_A:180,0,346	chr1	14610	14610	T	C	ncRNA_exonic	WASH7P				intergenic	NONE,MIR6859-3	dist=NONE;dist=2759																																																																						0.0001921	5	26028		chr1:14610:14610:T:C	1	0.5	3.16	0	13	no_DS	no_END	3.0103	3.123	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	31	-1.44E+00	11.67	no_RAW_MQ	0.86	2.03	TGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAG[T]AGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAA	pass	XX	.	0	1	0
chr1	14653	.	C	T	254.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.91;ClippingRankSum=0.00;DP=25;ExcessHet=3.0103;FS=7.952;MLEAC=1;MLEAF=0.500;MQ=30.99;MQRankSum=-1.236e+00;QD=10.19;ReadPosRankSum=0.792;SOR=2.642	GT:AD:DP:GQ:PL	0/1:12,13:25:99:283,0,238	chr1	14653	14653	C	T	ncRNA_exonic	WASH7P				intergenic	NONE,MIR6859-3	dist=NONE;dist=2716			rs62635297																																																																			0.0011526	30	26028		chr1:14653:14653:C:T	1	0.5	1.91	0	25	no_DS	no_END	3.0103	7.952	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	30.99	-1.24E+00	10.19	no_RAW_MQ	0.792	2.642	AAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAA[C]GGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATT	pass	XX	.	0	1	0
chr1	16949	.	A	C	183.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.580e-01;ClippingRankSum=0.00;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.07;MQRankSum=-1.095e+00;QD=5.93;ReadPosRankSum=-3.240e-01;SOR=0.515	GT:AD:DP:GQ:PL	0/1:19,12:31:99:212,0,396	chr1	16949	16949	A	C	ncRNA_exonic	WASH7P				downstream	MIR6859-3				rs199745162	0.0139776	0.0227	0.0144	0.0143	0.0159																																																														0.0159444	415	26028		chr1:16949:16949:A:C	1	0.5	-7.58E-01	0	31	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	21.07	-1.10E+00	5.93	no_RAW_MQ	-3.24E-01	0.515	CTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCA[A]TGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGA	pass	XX	.	0	1	0
chr1	17020	.	G	A	99.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.024e+00;ClippingRankSum=0.00;DP=26;ExcessHet=3.0103;FS=14.474;MLEAC=1;MLEAF=0.500;MQ=21.00;MQRankSum=0.00;QD=3.84;ReadPosRankSum=-2.034e+00;SOR=2.800	GT:AD:DP:GQ:PL	0/1:18,8:26:99:128,0,424	chr1	17020	17020	G	A	ncRNA_exonic	WASH7P				downstream	MIR6859-3				rs199740902																																																																			0.0141002	367	26028		chr1:17020:17020:G:A	1	0.5	-1.02E+00	0	26	no_DS	no_END	3.0103	14.474	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	21	0	3.84	no_RAW_MQ	-2.03E+00	2.8	ATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG[G]CCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCA	pass	XX	.	0	1	0
chr1	17365	.	C	G	154.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.621;ClippingRankSum=0.00;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.91;MQRankSum=-1.245e+00;QD=3.60;ReadPosRankSum=-1.701e+00;SOR=0.485	GT:AD:DP:GQ:PGT:PID:PL	0/1:36,7:43:99:0|1:17365_C_G:183,0,2051	chr1	17365	17365	C	G	ncRNA_exonic	WASH7P				downstream	MIR6859-3				rs369606208										0.2553	0.1603	0.221	0.3841	0.2245	0.2715	0.2581	0.2883																																																		7.76E-05	12	154602		chr1:17365:17365:C:G	1	0.5	0.621	0	43	no_DS	no_END	3.0103	0	no_HaplotypeScore	no_InbreedingCoeff	1	0.5	43.91	-1.25E+00	3.6	no_RAW_MQ	-1.70E+00	0.485	TGGGTCTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTT[C]TACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTG	pass	XX	.	0	1	0