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comparison test-data/vcfvcfintersect-test1.vcf @ 1:fabee003a629 draft default tip

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author anton
date Wed, 11 Jun 2014 16:42:03 -0400
parents 1457784cf167
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0:1457784cf167 1:fabee003a629
1 ##fileformat=VCFv4.0 1 ##fileformat=VCFv4.1
2 ##fileDate=20090805 2 ##fileDate=20140610
3 ##source=myImputationProgramV3.1 3 ##source=Dan
4 ##reference=1000GenomesPilot-NCBI36 4 ##reference=file:///galaxy/data/phiX/sam_index/phiX.fa
5 ##phasing=partial 5 ##filter="AF > .001"
6 ##filter="QUAL > 1" 6 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
7 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> 7 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
8 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
9 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
10 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
11 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
12 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
13 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
14 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
15 ##FILTER=<ID=q10,Description="Quality below 10">
16 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
17 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
18 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 9 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
19 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> 10 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
20 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> 11 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
21 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> 12 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB
22 ##ALT=<ID=CNV,Description="Copy number variable region"> 13 phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2,
23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 14 phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1,
24 X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 15 phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28,
16 phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28,
17 phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2,
18 phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32,
19 phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34,
20 phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1,
21 phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3,
22 phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1,
23 phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1,
24 phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45,