Mercurial > repos > devteam > realigner_target_creator

annotate test-data/gatk/fake_phiX_variant_locations.vcf @ 1:f202477a521b default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix JAVA_JAR_PATH.
author Dave Bouvier <dave@bx.psu.edu>
date Fri, 04 Apr 2014 10:27:08 -0400
parents 751f4d177d8e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
1 ##fileformat=VCFv4.1
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
2 ##samtoolsVersion=0.1.18 (r982:295)
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
5 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
6 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
7 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
8 ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
9 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
10 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
11 ##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
12 ##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
13 ##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
14 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
15 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
16 ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
17 ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
18 ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
19 ##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
20 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
21 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
22 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
23 ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
24 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
25 ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
26 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
27 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
28 phiX174 1411 . A . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
29 phiX174 1412 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
30 phiX174 1413 . C . 28.2 . DP=5;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
31 phiX174 1414 . G . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
32 phiX174 1415 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
33 phiX174 1416 . C . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
34 phiX174 1417 . G . 28.2 . DP=9;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
35 phiX174 1418 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
36 phiX174 1419 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
37 phiX174 1420 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
38 phiX174 1421 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
39 phiX174 1422 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
40 phiX174 1423 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
41 phiX174 1424 . C . 28.2 . DP=10;VDB=0.0005;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
42 phiX174 1425 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
43 phiX174 1426 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
44 phiX174 1427 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
45 phiX174 1428 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
46 phiX174 1429 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
47 phiX174 1430 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
48 phiX174 1431 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
49 phiX174 1432 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
50 phiX174 1433 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
51 phiX174 1434 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
52 phiX174 1435 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
53 phiX174 1436 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
54 phiX174 1437 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
55 phiX174 1438 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
56 phiX174 1439 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
57 phiX174 1440 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
58 phiX174 1441 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
59 phiX174 1442 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
60 phiX174 1443 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
61 phiX174 1444 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
62 phiX174 1445 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
63 phiX174 1446 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
64 phiX174 1447 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
65 phiX174 1448 . A . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
66 phiX174 1449 . A . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
67 phiX174 1450 . T . 28.2 . DP=4;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
68 phiX174 1451 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
69 phiX174 1452 . A . 28.2 . DP=2;;AC1=2;FQ=-30 PL 0
751f4d177d8e Imported from capsule None
devteam
parents:
diff changeset
70 phiX174 1453 . G . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0