Mercurial > repos > jjohnson > bcftools_convert_from_vcf

comparison test-data/view.GL.vcf @ 0:d396503fdbdb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:47:20 -0400
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-1:000000000000 0:d396503fdbdb
1 ##fileformat=VCFv4.1
2 ##FILTER=<ID=PASS,Description="All filters passed">
3 ##reference=file:///seq/references/1000Genomes-NCBI37.fasta
4 ##contig=<ID=11,length=135006516>
5 ##contig=<ID=20,length=63025520>
6 ##contig=<ID=X,length=155270560>
7 ##contig=<ID=Y,length=59373566>
8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="List of Phred-scaled genotype likelihoods">
9 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
10 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
11 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
12 ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
13 ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
14 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
15 11 2343543 . A . 999 PASS . GL 0,-25.5,-25.5 0,-25.5,-25.5 0,-25.5,-25.5
16 11 5464562 . C T 999 PASS . GL 0,0,0 0,0,0 0,0,0
17 20 76962 rs6111385 T C 999 PASS . GL -25.5,0,-25.5 -25.5,-25.5,0 -25.5,-25.5,0
18 20 126310 . ACC A 999 StrandBias;EndDistBias . GL -25.5,0,-13.2 -25.5,0,-13.9 -25.5,-21.3,0
19 20 138125 rs2298108 G T 999 PASS . GL -13.5,0,-16.3 -14,0,-25.5 -25.5,-19.9,0
20 20 138148 rs2298109 C T 999 PASS . GL -19.5,0,-25.5 -19.2,0,-25.5 -25.5,-23.5,0
21 20 271225 . T TTTA,TA 999 StrandBias . GL -15.1,-5.3,-20.3,0,-5.2,-15.9 -25.5,0,-21.3,-25.5,-25.5,-25.5 -25.5,-25.5,-25.5,-25.5,0,-24.1
22 20 304568 . C T 999 PASS . GL -9.5,0,-25.5 -19.2,0,-25.5 -25.5,-9.5,0
23 20 326891 . A AC 999 PASS . GL -25.5,0,-13.2 -25.5,0,-13.9 .,.,.
24 X 2928329 rs62584840 C T 999 PASS . GL 0,-5.6 0,-8.1 -7.3,0,-1.9
25 X 2933066 rs61746890 G C 999 PASS . GL 0,-25.5 0,-25.5 -25.5,-25.5,-25.5
26 X 2942109 rs5939407 T C 999 PASS . GL 0,-25.5 -25.5,0 -25.5,-15.7,0
27 X 3048719 . T C 999 PASS . GL 0,-25.5 -25.5,0 -25.5,0,-15.7
28 Y 8657215 . C A 999 PASS . GL 0,-25.5 -25.5,0 .
29 Y 10011673 rs78249411 G A 999 MinAB . GL -12.6,-10.1 -9.5,0 .