Mercurial > repos > devteam > variant_eval
diff test-data/gatk/fake_phiX_variant_locations.vcf @ 0:fbca1c0956d2 draft default tip
Imported from capsule None
| author | devteam |
|---|---|
| date | Tue, 01 Apr 2014 10:49:25 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gatk/fake_phiX_variant_locations.vcf Tue Apr 01 10:49:25 2014 -0400 @@ -0,0 +1,70 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.18 (r982:295) +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> +##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> +##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> +##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> +##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> +##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> +##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> +##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> +##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> +##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> +##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> +##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> +##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> +##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample +phiX174 1411 . A . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0 +phiX174 1412 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0 +phiX174 1413 . C . 28.2 . DP=5;;AC1=2;FQ=-30 PL 0 +phiX174 1414 . G . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0 +phiX174 1415 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0 +phiX174 1416 . C . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0 +phiX174 1417 . G . 28.2 . DP=9;;AC1=2;FQ=-30 PL 0 +phiX174 1418 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1419 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1420 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1421 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1422 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1423 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1424 . C . 28.2 . DP=10;VDB=0.0005;;AC1=2;FQ=-30 PL 0 +phiX174 1425 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1426 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1427 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1428 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1429 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1430 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1431 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1432 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1433 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1434 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1435 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1436 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1437 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1438 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1439 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1440 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1441 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1442 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1443 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1444 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0 +phiX174 1445 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1446 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1447 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0 +phiX174 1448 . A . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0 +phiX174 1449 . A . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0 +phiX174 1450 . T . 28.2 . DP=4;;AC1=2;FQ=-30 PL 0 +phiX174 1451 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0 +phiX174 1452 . A . 28.2 . DP=2;;AC1=2;FQ=-30 PL 0 +phiX174 1453 . G . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0