Mercurial > repos > blankenberg > naive_variant_caller

comparison test-data/fake_phiX174_reads_1_test_out_1.vcf @ 16:07e71cf6c8ef draft

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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
author blankenberg
date Tue, 03 Apr 2018 10:52:11 -0400
parents ae6edc0012ba
children
comparison
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15:aff38ea879f1 16:07e71cf6c8ef
1 ##fileformat=VCFv4.1 1 ##fileformat=VCFv4.3
2 ##source=Naive Variant Caller version 0.0.4
2 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> 3 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
3 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> 4 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
5 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> 6 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
6 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> 7 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
7 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> 8 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
8 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample 9 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample
9 phiX174 1411 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=1, 10 phiX174 1411 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=1,
10 phiX174 1412 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=3, 11 phiX174 1412 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=3,
11 phiX174 1413 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=5, 12 phiX174 1413 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=5,
12 phiX174 1414 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=6, 13 phiX174 1414 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=6,
13 phiX174 1415 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=7, 14 phiX174 1415 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=7,
14 phiX174 1416 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=8, 15 phiX174 1416 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=8,
15 phiX174 1417 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=9, 16 phiX174 1417 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=9,
16 phiX174 1418 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, 17 phiX174 1418 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10,
17 phiX174 1419 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 18 phiX174 1419 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
18 phiX174 1420 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 19 phiX174 1420 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
19 phiX174 1421 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, 20 phiX174 1421 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10,
20 phiX174 1422 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, 21 phiX174 1422 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10,
21 phiX174 1423 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 22 phiX174 1423 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
22 phiX174 1424 . C A . . AC=7;AF=0.7 GT:AC:AF:NC 1/0:7:0.7:A=7,C=3, 23 phiX174 1424 . C A . . AC=7;AF=0.7 GT:AC:AF:NC 1/0:7:0.7:A=7,C=3,
23 phiX174 1425 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 24 phiX174 1425 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
24 phiX174 1426 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, 25 phiX174 1426 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10,
25 phiX174 1427 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 26 phiX174 1427 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
26 phiX174 1428 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, 27 phiX174 1428 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10,
27 phiX174 1429 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 28 phiX174 1429 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
28 phiX174 1430 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 29 phiX174 1430 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
29 phiX174 1431 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 30 phiX174 1431 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
30 phiX174 1432 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, 31 phiX174 1432 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10,
31 phiX174 1433 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, 32 phiX174 1433 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10,
32 phiX174 1434 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 33 phiX174 1434 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
33 phiX174 1435 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 34 phiX174 1435 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
34 phiX174 1436 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 35 phiX174 1436 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
35 phiX174 1437 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, 36 phiX174 1437 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10,
36 phiX174 1438 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 37 phiX174 1438 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
37 phiX174 1439 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10, 38 phiX174 1439 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=10,
38 phiX174 1440 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 39 phiX174 1440 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
39 phiX174 1441 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10, 40 phiX174 1441 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=10,
40 phiX174 1442 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, 41 phiX174 1442 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10,
41 phiX174 1443 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10, 42 phiX174 1443 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=10,
42 phiX174 1444 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 43 phiX174 1444 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
43 phiX174 1445 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10, 44 phiX174 1445 . C . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:C=10,
44 phiX174 1446 . C T . . AC=3;AF=0.3 GT:AC:AF:NC 0/1:3:0.3:C=7,T=3, 45 phiX174 1446 . C T . . AC=3;AF=0.3 GT:AC:AF:NC 0/1:3:0.3:C=7,T=3,
45 phiX174 1447 . T A . . AC=2;AF=0.222222222222 GT:AC:AF:NC 0/0:2:0.222222222222:A=2,T=7, 46 phiX174 1447 . T A . . AC=2;AF=0.222222222222 GT:AC:AF:NC 0/0:2:0.222222222222:A=2,T=7,
46 phiX174 1448 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=7, 47 phiX174 1448 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=7,
47 phiX174 1449 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=5, 48 phiX174 1449 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=5,
48 phiX174 1450 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=4, 49 phiX174 1450 . T . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:T=4,
49 phiX174 1451 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=3, 50 phiX174 1451 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=3,
50 phiX174 1452 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=2, 51 phiX174 1452 . A . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:A=2,
51 phiX174 1453 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=1, 52 phiX174 1453 . G . . . AC=.;AF=. GT:AC:AF:NC 0/0:.:.:G=1,