Mercurial > repos > iuc > fermikit_variants

annotate test-data/flt.vcf @ 1:ed056d243455 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit ab4afb50e6c991cc2e784a93a0c7a75329eac88c
author iuc
date Mon, 27 Jun 2022 11:22:33 +0000
parents 44519e762f16
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.1
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
2 ##source=htsbox-pileup-r327
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
3 ##reference=/tmp/tmpIcvwsb/files/000/dataset_2.dat
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
4 ##contig=<ID=11_1910000_1940000,length=30001>
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
6 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
7 ##INFO=<ID=_DP,Number=1,Type=Integer,Description="Raw read depth">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
8 ##INFO=<ID=_DS,Number=1,Type=Integer,Description="min{alt_DP_on_forward, alt_DP_on_reverse}">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
9 ##INFO=<ID=_AB,Number=1,Type=Integer,Description="Percentage of non-reference reads">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
10 ##INFO=<ID=_FS,Number=1,Type=Integer,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
11 ##FILTER=<ID=DPhigh,Description="High read depth: _DP>62.82">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
12 ##FILTER=<ID=DPlow,Description="Low read depth: _DP<3">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
13 ##FILTER=<ID=FShigh,Description="Large Fisher-Strand bias: _FS>30">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
14 ##FILTER=<ID=ABlow,Description="Low fraction of non-reference reads: _AB<30 at SNPs or _AB<30 at INDELs">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
15 ##FILTER=<ID=DSlow,Description="Low double-strand support at SNPs: _DS<1">
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
16 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aligned_contigs_bam
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
17 11_1910000_1940000 636 . c T 25 . _DP=39;_AB=64 GT:AD 1/0:14,25
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
18 11_1910000_1940000 708 . t C 40 . _DP=40;_AB=100 GT:AD 1/1:0,40
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
19 11_1910000_1940000 1116 . t C 43 . _DP=43;_AB=100 GT:AD 1/1:0,43
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
20 11_1910000_1940000 1891 . t C 44 . _DP=44;_AB=100 GT:AD 1/1:0,44
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
21 11_1910000_1940000 2297 . a G 43 . _DP=43;_AB=100 GT:AD 1/1:0,43
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
22 11_1910000_1940000 2727 . a G 42 . _DP=42;_AB=100 GT:AD 1/1:0,42
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
23 11_1910000_1940000 3378 . a G 50 . _DP=50;_AB=100 GT:AD 1/1:0,50
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
24 11_1910000_1940000 4140 . c T 21 . _DP=36;_AB=58 GT:AD 1/0:15,21
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
25 11_1910000_1940000 4820 . g A 35 . _DP=35;_AB=100 GT:AD 1/1:0,35
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
26 11_1910000_1940000 4860 . t G 36 . _DP=36;_AB=100 GT:AD 1/1:0,36
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
27 11_1910000_1940000 4976 . g A 33 . _DP=33;_AB=100 GT:AD 1/1:0,33
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
28 11_1910000_1940000 5455 . a AGT 12 . _DP=25;_AB=48 GT:AD 0/1:13,12
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
29 11_1910000_1940000 5559 . g T 39 . _DP=39;_AB=100 GT:AD 1/1:0,39
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
30 11_1910000_1940000 6369 . ct C 8 ABlow _DP=42;_AB=19 GT:AD 0/1:34,8
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
31 11_1910000_1940000 6654 . g A 43 . _DP=43;_AB=100 GT:AD 1/1:0,43
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
32 11_1910000_1940000 7873 . g A 45 . _DP=45;_AB=100 GT:AD 1/1:0,45
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
33 11_1910000_1940000 8084 . t C 54 . _DP=54;_AB=100 GT:AD 1/1:0,54
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
34 11_1910000_1940000 10894 . t G 40 . _DP=40;_AB=100 GT:AD 1/1:0,40
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
35 11_1910000_1940000 12259 . a G 35 . _DP=35;_AB=100 GT:AD 1/1:0,35
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
36 11_1910000_1940000 15695 . g A 36 . _DP=36;_AB=100 GT:AD 1/1:0,36
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
37 11_1910000_1940000 16353 . ctt C 14 . _DP=14;_AB=100 GT:AD 1/1:0,14
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
38 11_1910000_1940000 20714 . c T 24 . _DP=42;_AB=57 GT:AD 1/0:18,24
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
39 11_1910000_1940000 24531 . t G 32 . _DP=32;_AB=100 GT:AD 1/1:0,32
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
40 11_1910000_1940000 24546 . gt G 25 . _DP=25;_AB=100 GT:AD 1/1:0,25
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
41 11_1910000_1940000 25710 . t TTG 17 . _DP=46;_AB=37 GT:AD 0/1:29,17
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
42 11_1910000_1940000 25813 . c CTG,CTGTG 13 . _DP=33;_AB=70 GT:AD 1/0:10,13,10
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
43 11_1910000_1940000 26084 . ctg C,CTGTGTG 17 . _DP=36;_AB=75 GT:AD 1/2:9,17,10
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
44 11_1910000_1940000 26212 . g A 29 . _DP=55;_AB=53 GT:AD 1/0:26,29
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
45 11_1910000_1940000 26370 . c CTG,CTGTGTG 12 . _DP=34;_AB=68 GT:AD 1/0:11,12,11
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
46 11_1910000_1940000 26521 . a G 30 . _DP=30;_AB=100 GT:AD 1/1:0,30
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
47 11_1910000_1940000 26713 . a G 32 . _DP=32;_AB=100 GT:AD 1/1:0,32
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
48 11_1910000_1940000 27735 . tc T 41 . _DP=41;_AB=100 GT:AD 1/1:0,41
44519e762f16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff changeset
49 11_1910000_1940000 28524 . c A 18 . _DP=38;_AB=47 GT:AD 0/1:20,18