ngs_server 0.1 → 0.2

data/ext/vcftools/examples/.svn/text-base/valid-3.3.vcf.svn-base

@@ -0,0 +1,30 @@
+##fileformat=VCFv3.3
+##fileDate=20090805
+##phasing=partial
+##test meta
+##INFO=NS,1,Integer,"Number of Samples With Data"
+##INFO=DP,1,Integer,"Total Depth"
+##INFO=AN,1,Integer,"Total number of alleles in called genotypes"
+##INFO=AC,-1,Integer,"Allele count in genotypes, for each ALT allele, in the same order as listed"
+##INFO=AF,-1,Float,"Allele Frequency"
+##INFO=AA,1,String,"Ancestral Allele"
+##INFO=DB,0,Flag,"dbSNP membership, build 129"
+##INFO=H2,0,Flag,"HapMap2 membership"
+##FILTER=q10,"Quality below 10"
+##FILTER=s50,"Less than 50% of samples have data"
+##FORMAT=GT,1,String,"Genotype"
+##FORMAT=GQ,1,Integer,"Genotype Quality"
+##FORMAT=DP,1,Integer,"Read Depth"
+##FORMAT=HQ,2,Integer,"Haplotype Quality"
+##FORMAT=DS,1,Float,"Alternative Allele Dosage"
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+19	111	.	A	C	9.6	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
+19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
+20	14370	rs6054257	G	A	29	0	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:-1,-1
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:-1,-1
+20	1110696	rs6040355	A	G,T	67	0	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:-1,-1
+20	1230237	.	T	.	47	0	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:-1:56,60	0|0:48:4:51,51	0/0:61:2:-1,-1
+20	1234567	microsat1	G	D4,IGA	50	0	NS=3;DP=9;AA=G;AN=6;AC=3,1	GT:GQ:DP	0/1:-1:4	0/2:17:2	1/1:40:3
+20	1235237	.	T	.	-1	.	.	GT	0\0	0|0	./.
+X	10	rsTest	A	T	10	.	.	GT:DS	0:0.1	0/1:0.5	0|1:0.5
+X	11	rsTest2	T	A,G	10	q10;s50	.	GT:DP:GQ	0:3:10	.:5:20	0:3:10

data/ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.stats.svn-base

@@ -0,0 +1,104 @@
+$VAR1 = {
+          'samples' => {
+                         'NA00002' => {
+                                        'indel_count' => 2,
+                                        'indel' => {
+                                                     '2' => 1,
+                                                     '-1' => 1
+                                                   },
+                                        'het_RA_count' => 6,
+                                        'snp_count' => 5,
+                                        'count' => 11,
+                                        'hom_RR_count' => 4,
+                                        'ref' => 10,
+                                        'missing' => 1,
+                                        'private' => 1,
+                                        'phased' => 7,
+                                        'het_AA_count' => 1,
+                                        'snp' => {
+                                                   'A>G' => 1,
+                                                   'A>T' => 2,
+                                                   'T>A' => 2,
+                                                   'G>A' => 1
+                                                 },
+                                        'unphased' => 4,
+                                        'ref_count' => 10
+                                      },
+                         'NA00001' => {
+                                        'het_RA_count' => 1,
+                                        'indel_count' => 1,
+                                        'indel' => {
+                                                     '1' => 1
+                                                   },
+                                        'snp_count' => 1,
+                                        'count' => 11,
+                                        'hom_RR_count' => 9,
+                                        'ref' => 10,
+                                        'missing' => 1,
+                                        'phased' => 6,
+                                        'het_AA_count' => 1,
+                                        'snp' => {
+                                                   'A>T' => 1,
+                                                   'A>G' => 1
+                                                 },
+                                        'unphased' => 5,
+                                        'ref_count' => 10
+                                      },
+                         'NA00003' => {
+                                        'hom_AA_count' => 4,
+                                        'other_count' => 2,
+                                        'indel_count' => 1,
+                                        'indel' => {
+                                                     '1' => 1
+                                                   },
+                                        'het_RA_count' => 5,
+                                        'snp_count' => 6,
+                                        'count' => 11,
+                                        'hom_RR_count' => 2,
+                                        'ref' => 7,
+                                        'missing' => 1,
+                                        'private' => 3,
+                                        'phased' => 2,
+                                        'other' => 2,
+                                        'snp' => {
+                                                   'A>C' => 1,
+                                                   'A>T' => 2,
+                                                   'A>G' => 1,
+                                                   'T>A' => 1,
+                                                   'G>A' => 1
+                                                 },
+                                        'ref_count' => 7,
+                                        'unphased' => 9
+                                      }
+                       },
+          'all' => {
+                     'other_count' => 2,
+                     'indel_count' => 2,
+                     'indel' => {
+                                  '1' => 1,
+                                  '2' => 1,
+                                  '-1' => 1
+                                },
+                     'snp_count' => 8,
+                     'count' => 12,
+                     'ref' => 2,
+                     'nalt_0' => 2,
+                     'nalt_1' => 7,
+                     'shared' => {
+                                   '1' => 4,
+                                   '0' => 2,
+                                   '3' => 2,
+                                   '2' => 4
+                                 },
+                     'other' => 2,
+                     'nalt_2' => 3,
+                     'snp' => {
+                                'A>C' => 1,
+                                'A>T' => 2,
+                                'A>G' => 2,
+                                'T>A' => 3,
+                                'G>A' => 1
+                              },
+                     'ref_count' => 2
+                   }
+        };

data/ext/vcftools/examples/.svn/text-base/valid-4.0.vcf.svn-base

@@ -0,0 +1,34 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
+##ALT=<ID=CNV,Description="Copy number variable region">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+19	111	.	A	C	9.6	.	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
+19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0/1:3,3
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.,.
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.,.
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:.:56,60	0|0:48:4:51,51	0/0:61:2:.,.
+20	1234567	microsat1	G	GA,GAC	50	PASS	NS=3;DP=9;AA=G;AN=6;AC=3,1	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
+20	1235237	.	T	.	.	.	.	GT	0/0	0|0	./.
+X	9	.	A	T	12.1	.	.	GT	0	0/1	1/0
+X	10	rsTest	AC	A,ATG	10	PASS	.	GT	0	0/1	0|2
+X	11	rsTest2	T	A,<DEL:ME:ALU>	10	q10;s50	.	GT:DP:GQ	.:3:10	./.	0|2:3
+X	12	.	T	A	13	.	.	GT	0	1/0	1/1

data/ext/vcftools/examples/.svn/text-base/valid-4.1.vcf.svn-base

@@ -0,0 +1,37 @@
+##fileformat=VCFv4.1
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##FILTER=<ID=q10,Description="Quality below 10 (\"with quotes\")">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data (with \\ backslash)">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##reference=file:/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##contig=<ID=19,length=59128983,md5=1aacd71f30db8e561810913e0b72636d,species="Homo Sapiens">
+##contig=<ID=20,length=63025520,md5=0dec9660ec1efaaf33281c0d5ea2560f,species="Homo Sapiens">
+##SAMPLE=<ID=Blood,Genomes=Germline,Mixture=1.,Description="Patient germline genome">
+##SAMPLE=<ID=TissueSample,Genomes=Germline;Tumor,Mixture=.3;.7,Description="Patient germline genome;Patient tumor genome">
+##PEDIGREE=<Derived=ID2,Original=ID1>
+##PEDIGREE=<Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
+##pedigreeDB=url
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+19	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+20	1234567	microsat1	GTC	G,GTCTC	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
+20	2234567	.	C	[13:123457[ACGC	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
+20	2234568	.	C	.CT	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
+20	2234569	.	C	TC.	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3
+20	3234569	.	C	<INV>	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1/0:40:3
+20	4234569	.	N	.[13:123457[	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	./.:40:3
+20	5234569	.	N	[13:123457[.	50	PASS	SVTYPE=BND;NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/1:17:2	1/1:40:3

data/ext/vcftools/examples/annotate-test.vcf

@@ -0,0 +1,37 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	100	.	GTTT	G	1806	q10	DP=35
+1	104	.	C	.	1792	PASS	DP=32
+1	105	.	C	T	246	PASS	DP=10
+1	106	.	C	A	246	PASS	DP=10
+2	107	.	C	.	1806	q10	DP=35
+2	108	.	C	.	1792	PASS	DP=32
+2	109	.	C	.	628	q10	DP=21
+2	110	.	C	G	1016	PASS	DP=22
+2	111	.	C	G	727	PASS	DP=30
+2	112	.	C	G	246	PASS	DP=10
+2	113	.	C	.	246	PASS	DP=10
+2	114	.	T	.	246	PASS	DP=10
+2	115	.	T	.	246	PASS	DP=10
+2	116	.	T	.	246	PASS	DP=10
+2	117	.	T	A	246	PASS	DP=10
+2	118	.	T	C	246	PASS	DP=10
+2	119	.	TAAA	T	246	PASS	DP=10
+2	124	.	TA	T	246	PASS	DP=10
+2	128	.	T	TA	246	PASS	DP=10
+2	130	.	C 	A	246	PASS	DP=10
+2	131	.	T	A	246	PASS	DP=10
+2	132	.	T	A	246	PASS	DP=10
+2	133	.	T	A	246	PASS	DP=10
+2	134	.	T	A	246	PASS	DP=10
+2	135	.	T	C	246	PASS	DP=10
+2	136	.	TT	T	246	PASS	DP=10
+17	12412	.	CAGAGAGAGA	CAGAGAGAGAGA	74.8	.	INDEL;DP=5388;AF1=0.006576;CI95=0.005525,0.01105;DP4=2077,2367,21,22;MQ=47;FQ=74.8;PV4=0.88,1,0.34,0.021
+17	12427	.	G	A	999	.	DP=5557;AF1=0.06028;CI95=0.04972,0.07182;DP4=2461,2689,106,74;MQ=47;FQ=999;PV4=0.0038,1,2.6e-12,1
+17	69284	.	G	A	14.6	.	DP=3946;AF1=0.003468;CI95=0.002762,0.008287;DP4=1529,2177,7,9;MQ=44;FQ=14.6;PV4=1,0.035,0.098,1
+17	69293	.	GTTTCATTTC	GTTTCTTTTCATTTC	999	.	INDEL;DP=3568;AF1=0.1295;CI95=0.1077,0.1547;DP4=1014,1238,118,121;MQ=44;FQ=999;PV4=0.22,1,9.4e-54,1

data/ext/vcftools/examples/annotate.out

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+##INFO=<ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership">
+##INFO=<ID=GN,Number=1,Type=String,Description="Gene Name">
+##INFO=<ID=DP,Number=0,Type=Integer,Description="Depth,etc">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	.	GTTT	G	1806	q10	DP=5;GN=gene1;HM2	GT:GQ:DP	0/1:409:35
+1	110	.	CAAA	C	1792	PASS	DP=6	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=7;HM2	GT:GQ:DP	0/1:212:22
+1	140	.	GT	G	727	PASS	DP=8	GT:GQ:DP	0/1:150:30
+1	150	.	TAAAA	TA,T	246	PASS	DP=9	GT:GQ:DP	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	GN=gene2;HM2	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	GN=gene2;HM2	GT:GQ:DP	1/2:12:10
+2	160	.	TAAAA	TA,TC,T	246	PASS	DP=11;GN=gene3	GT:GQ:DP	0/2:12:10

data/ext/vcftools/examples/annotate.txt

@@ -0,0 +1,7 @@
+100	100	1	id1_100	.	.	HM2	gene1	5
+110	110	1	id1_110	CAAA	C	0	.	6
+130	130	1	id1_130	GAA	GG	HM2	.	7
+140	140	1	id1_140	GT	G	0	.	8
+150	150	1	id1_150	TAAAA	T	0	.	9
+110	150	2	id2_110_150	CAAA	C	HM2	gene2	.
+160	160	2	id2_160	TAAAA	TC	0	gene3	11

data/ext/vcftools/examples/annotate2.out

@@ -0,0 +1,52 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=SnpCluster,Description="Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases [win=3,count=2]">
+##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=MaxDP,Description="Maximum read depth (INFO/DP or INFO/DP4) [34]">
+##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [0]">
+##FILTER=<ID=MinMQ,Description="Minimum RMS mapping quality for SNPs (INFO/MQ) [10]">
+##FILTER=<ID=Qual,Description="Minimum value of the QUAL field [10]">
+##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+##FILTER=<ID=VDB,Description="Minimum Variant Distance Bias (INFO/VDB) [0.015]">
+##FILTER=<ID=GapWin,Description="Window size for filtering adjacent gaps [3]">
+##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
+##FILTER=<ID=SnpGap,Description="SNP within INT bp around a gap to be filtered [10]">
+##FILTER=<ID=MinDP,Description="Minimum read depth (INFO/DP or INFO/DP4) [2]">
+##FILTER=<ID=RefN,Description="Reference base is N []">
+##FILTER=<ID=HWE,Description="Minimum P-value for HWE (plus F<0) (INFO/HWE and INFO/G3) [0.0001]">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	100	.	GTTT	G	1806	q10;MaxDP	DP=35
+1	104	.	C	.	1792	PASS	DP=32
+1	105	.	C	T	246	SnpGap;SnpCluster	DP=10
+1	106	.	C	A	246	SnpGap;SnpCluster	DP=10
+2	107	.	C	.	1806	q10;MaxDP	DP=35
+2	108	.	C	.	1792	PASS	DP=32
+2	109	.	C	.	628	q10	DP=21
+2	110	.	C	G	1016	SnpGap;SnpCluster	DP=22
+2	111	.	C	G	727	SnpGap;SnpCluster	DP=30
+2	112	.	C	G	246	SnpGap;SnpCluster	DP=10
+2	113	.	C	.	246	PASS	DP=10
+2	114	.	T	.	246	PASS	DP=10
+2	115	.	T	.	246	PASS	DP=10
+2	116	.	T	.	246	PASS	DP=10
+2	117	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	118	.	T	C	246	SnpGap;SnpCluster	DP=10
+2	119	.	TAAA	T	246	GapWin;SnpCluster	DP=10
+2	124	.	TA	T	246	GapWin	DP=10
+2	128	.	T	TA	246	SnpCluster	DP=10
+2	130	.	C 	A	246	SnpGap;SnpCluster	DP=10
+2	131	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	132	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	133	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	134	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	135	.	T	C	246	SnpGap;SnpCluster	DP=10
+2	136	.	TT	T	246	SnpCluster	DP=10
+17	12412	.	CAGAGAGAGA	CAGAGAGAGAGA	74.8	MaxDP	INDEL;DP=5388;AF1=0.006576;CI95=0.005525,0.01105;DP4=2077,2367,21,22;MQ=47;FQ=74.8;PV4=0.88,1,0.34,0.021
+17	12427	.	G	A	999	MaxDP;SnpGap	DP=5557;AF1=0.06028;CI95=0.04972,0.07182;DP4=2461,2689,106,74;MQ=47;FQ=999;PV4=0.0038,1,2.6e-12,1
+17	69284	.	G	A	14.6	MaxDP;SnpGap	DP=3946;AF1=0.003468;CI95=0.002762,0.008287;DP4=1529,2177,7,9;MQ=44;FQ=14.6;PV4=1,0.035,0.098,1
+17	69293	.	GTTTCATTTC	GTTTCTTTTCATTTC	999	MaxDP	INDEL;DP=3568;AF1=0.1295;CI95=0.1077,0.1547;DP4=1014,1238,118,121;MQ=44;FQ=999;PV4=0.22,1,9.4e-54,1

data/ext/vcftools/examples/annotate3.out

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+##INFO=<ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership">
+##INFO=<ID=GN,Number=1,Type=String,Description="Gene Name">
+##INFO=<ID=DP,Number=0,Type=Integer,Description="Depth,etc">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	id1_100	GTTT	G	1806	q10	DP=5;GN=gene1;HM2	GT:GQ:DP	0/1:409:35
+1	110	id1_110	CAAA	C	1792	PASS	DP=6	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	140	id1_140	GT	G	727	PASS	DP=8	GT:GQ:DP	0/1:150:30
+1	150	id1_150	TAAAA	TA,T	246	PASS	DP=9	GT:GQ:DP	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	id2_110_150	CAAA	C	1792	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	160	id2_160	TAAAA	TA,TC,T	246	PASS	DP=11;GN=gene3	GT:GQ:DP	0/2:12:10

data/ext/vcftools/examples/cmp-test-a-3.3.vcf

@@ -0,0 +1,12 @@
+##fileformat=VCFv3.3
+##INFO=DP,1,Integer,"Total Depth"
+##FORMAT=GT,1,String,"Genotype"
+##FORMAT=GQ,1,Integer,"Genotype Quality"
+##FORMAT=DP,1,Integer,"Read Depth"
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/1:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	./.:40:1
+1	100400	.	C	G,T	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/2:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/cmp-test-a.vcf

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/1:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	./.:40:1
+1	100400	.	C	G,T	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/2:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/cmp-test-b-3.3.vcf

@@ -0,0 +1,12 @@
+##fileformat=VCFv3.3
+##INFO=DP,1,Integer,"Total Depth"
+##FORMAT=GT,1,String,"Genotype"
+##FORMAT=GQ,1,Integer,"Genotype Quality"
+##FORMAT=DP,1,Integer,"Read Depth"
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	1/0:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	1|0:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100400	.	C	G	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/0:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/cmp-test-b.vcf

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	1/0:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	1|0:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100400	.	C	G	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/0:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/cmp-test.out

@@ -0,0 +1,53 @@
+# This file was generated by vcf-compare.
+#
+#VN 'Venn-Diagram Numbers'. Use `grep ^VN | cut -f 2-` to extract this part.
+#VN The columns are: 
+#VN        1  .. number of sites unique to this particular combination of files
+#VN        2- .. combination of files and space-separated number, a fraction of sites in the file
+VN	6	cmp-test-a.vcf.gz (100.0%)	cmp-test-b.vcf.gz (100.0%)
+#SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
+SN	Number of REF matches:	6
+SN	Number of ALT matches:	5
+SN	Number of REF mismatches:	0
+SN	Number of ALT mismatches:	1
+SN	Number of samples in GT comparison:	2
+#GS Genotype Comparison Summary. Use `grep ^GS | cut -f 2-` to extract this part.
+#GS The columns are:
+#GS        1  .. variant type
+#GS        2  .. number of mismatches
+#GS        3  .. number of matches
+#GS        4  .. discordance
+GS	hom_RR	0	3	0.00%
+GS	het_RA	1	3	25.00%
+GS	hom_AA	0	4	0.00%
+GS	het_AA	0	0	0.00%
+SN	Non-reference Discordance Rate (NDR):	12.50
+
+#GC Genotype Comparison. Use `grep ^GC | cut -f 2-` to extract this part.
+#GC The columns are:
+#GC       1     .. Sample
+#GC       2-6   .. Gtype mismatches: total hom_RR hom_AA het_RA het_AA 
+#GC       7-9   .. Gtype lost: total het_RA het_AA 
+#GC       10-14 .. Gtype gained: total hom_RR hom_AA het_RA het_AA 
+#GC       15-17 .. Phase lost: total het_RA het_AA 
+#GC       18    .. Phase gained
+#GC       19-23 .. Matching sites: total hom_RR hom_AA het_RA het_AA 
+#GC       24-26 .. Phased matches: total het_RA het_AA 
+#GC       27-29 .. Misphased matches: total het_RA het_AA 
+GC	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	4	2	0	1	1	0	0	0	0
+GC	B	1	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	4	3	0	1	0	0	0	0	0	0	0
+#FC Genotype Concordance vs non-ref allele frequency. Use `^FC | cut -f 2-` to extract this part.
+#FC The columns are:
+#FC      1  .. Non-ref allele count
+#FC      2  .. Hom(RR) concordance
+#FC      3  .. Het(RA) concordance
+#FC      4  .. Hom(AA) concordance
+#FC      5  .. Het(AA) concordance
+#FC      6  .. Number of Hom(RR) gtypes
+#FC      7  .. Number of Het(RA) gtypes
+#FC      8  .. Number of Hom(AA) gtypes
+#FC      9  .. Number of Het(AA) gtypes
+FC	0.25	1.000	1.000	-1.000	-1.000	1	1	0	0
+FC	0.50	1.000	1.000	1.000	-1.000	2	2	2	0
+FC	0.75	-1.000	0.000	1.000	-1.000	0	1	1	0
+FC	1.00	-1.000	-1.000	1.000	-1.000	0	0	1	0

data/ext/vcftools/examples/concat-a.vcf

@@ -0,0 +1,21 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	160	.	TAAAA	TA,TC,T	246	PASS	DP=10	GT:GQ:DP	0/2:12:10

data/ext/vcftools/examples/concat-b.vcf

@@ -0,0 +1,13 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	141	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	151	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	161	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	171	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	181	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	191	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/concat-c.vcf

@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+2	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/concat.out

@@ -0,0 +1,39 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	141	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	151	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	161	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	171	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	181	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	191	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	160	.	TAAAA	TA,TC,T	246	PASS	DP=10	GT:GQ:DP	0/2:12:10
+2	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/invalid-4.0.vcf

@@ -0,0 +1,31 @@
+##fileformat=VCFv4.0
+##problem1=The first base of the second ALT allele at 20:1234567 does not match the reference.
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AC,Number=-1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=-1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description=Genotype>
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+19	111	.	A	C	9.6	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
+19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
+20	14370	rs6054257	G	A	29	0	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:-1,-1
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:-1,-1
+20	1110696	rs6040355	A	G,T	67	0	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:-1,-1
+20	1230237	.	T	.	47	0	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:-1:56,60	0|0:48:4:51,51	0/0:61:2:-1,-1
+20	1234567	microsat1	G	GA,AAC	50	0	NS=3;DP=9;AA=G;AN=6;AC=3,1	GT:GQ:DP	0/1:-1:4	0/2:17:2	1/1:40:3
+20	1235237	.	T	.	-1	.	.	GT	0\0	0|0	./.
+X	10	rsTest	AC	A,ATG	10	.	.	GT	0	0/1	0|2
+X	11	rsTest2	T	A,G	10	q10;s50	.	GT:DP:GQ	0:3:10	.:5:20	0:3:10

data/ext/vcftools/examples/isec-n2-test.vcf.out

@@ -0,0 +1,19 @@
+Warning: The column names do not match (e.g. B):
+B
+A
+##fileformat=VCFv4.0
+##FILTER=<ID=q10,Description="Quality below 10">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q20,Description="Mapping quality below 20">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	3062915	.	GTTT	G	1806	q10	DP=35;SF=0f,1f,2	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	1792	PASS	DP=32;SF=0,1,2	GT:GQ:DP	0/1:245:32
+1	3157410	.	GA	G	628	q10	DP=21;SF=0f,1,2	GT:GQ:DP	1/1:21:21
+1	3162006	.	GAA	G	1016	PASS	DP=22;SF=0,1,2	GT:GQ:DP	0/1:212:22
+1	3177144	.	GT	G	727	PASS	DP=30;SF=0,1,2	GT:GQ:DP	0/1:150:30
+1	3184885	.	TAAAA	TA,T	246	PASS	DP=10;SF=0,1	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/merge-test-a.vcf

@@ -0,0 +1,17 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	3062915	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	3157410	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	3162006	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	3177144	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	3184885	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	3199812	.	G	GTT,GT	481	PASS	DP=26	GT:GQ:DP	1/2:322:26
+3	3212016	.	CTT	C,CT	565	PASS	DP=26	GT:GQ:DP	1/2:91:26
+4	3258448	.	TACACACAC	T	325	PASS	DP=31	GT:GQ:DP	0/1:325:31