Mercurial > repos > anton > vcfdistance

annotate test-data/vcfdistance-test1.vcf @ 3:49482c68e701 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author anton
date Mon, 15 Sep 2014 14:50:50 -0400
parents de3bbf60d086
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
1 ##fileformat=VCFv4.0
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
2 ##fileDate=20090805
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
3 ##source=myImputationProgramV3.1
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
4 ##reference=1000GenomesPilot-NCBI36
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
5 ##phasing=partial
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
8 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
14 ##FILTER=<ID=q10,Description="Quality below 10">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
21 ##ALT=<ID=CNV,Description="Copy number variable region">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
22 ##INFO=<ID=BasesToClosestVariant,Number=1,Type=Integer,Description="Number of bases to the closest variant in the file.">
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
24 19 111 . A C 9.6 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
25 19 112 . A G 10 . BasesToClosestVariant=1 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
26 20 17330 . T A 3 q10 AF=0.017;BasesToClosestVariant=1093366;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,.
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
27 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BasesToClosestVariant=119541;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
28 20 1230237 . T . 47 PASS AA=T;BasesToClosestVariant=4330;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
de3bbf60d086 Imported from capsule None
anton
parents:
diff changeset
29 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;BasesToClosestVariant=670;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3