Mercurial > repos > iuc > fermikit_variants
diff test-data/flt.vcf @ 0:44519e762f16 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
| author | iuc |
|---|---|
| date | Thu, 05 Jan 2017 08:35:48 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flt.vcf Thu Jan 05 08:35:48 2017 -0500 @@ -0,0 +1,49 @@ +##fileformat=VCFv4.1 +##source=htsbox-pileup-r327 +##reference=/tmp/tmpIcvwsb/files/000/dataset_2.dat +##contig=<ID=11_1910000_1940000,length=30001> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##INFO=<ID=_DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=_DS,Number=1,Type=Integer,Description="min{alt_DP_on_forward, alt_DP_on_reverse}"> +##INFO=<ID=_AB,Number=1,Type=Integer,Description="Percentage of non-reference reads"> +##INFO=<ID=_FS,Number=1,Type=Integer,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> +##FILTER=<ID=DPhigh,Description="High read depth: _DP>62.82"> +##FILTER=<ID=DPlow,Description="Low read depth: _DP<3"> +##FILTER=<ID=FShigh,Description="Large Fisher-Strand bias: _FS>30"> +##FILTER=<ID=ABlow,Description="Low fraction of non-reference reads: _AB<30 at SNPs or _AB<30 at INDELs"> +##FILTER=<ID=DSlow,Description="Low double-strand support at SNPs: _DS<1"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT aligned_contigs_bam +11_1910000_1940000 636 . c T 25 . _DP=39;_AB=64 GT:AD 1/0:14,25 +11_1910000_1940000 708 . t C 40 . _DP=40;_AB=100 GT:AD 1/1:0,40 +11_1910000_1940000 1116 . t C 43 . _DP=43;_AB=100 GT:AD 1/1:0,43 +11_1910000_1940000 1891 . t C 44 . _DP=44;_AB=100 GT:AD 1/1:0,44 +11_1910000_1940000 2297 . a G 43 . _DP=43;_AB=100 GT:AD 1/1:0,43 +11_1910000_1940000 2727 . a G 42 . _DP=42;_AB=100 GT:AD 1/1:0,42 +11_1910000_1940000 3378 . a G 50 . _DP=50;_AB=100 GT:AD 1/1:0,50 +11_1910000_1940000 4140 . c T 21 . _DP=36;_AB=58 GT:AD 1/0:15,21 +11_1910000_1940000 4820 . g A 35 . _DP=35;_AB=100 GT:AD 1/1:0,35 +11_1910000_1940000 4860 . t G 36 . _DP=36;_AB=100 GT:AD 1/1:0,36 +11_1910000_1940000 4976 . g A 33 . _DP=33;_AB=100 GT:AD 1/1:0,33 +11_1910000_1940000 5455 . a AGT 12 . _DP=25;_AB=48 GT:AD 0/1:13,12 +11_1910000_1940000 5559 . g T 39 . _DP=39;_AB=100 GT:AD 1/1:0,39 +11_1910000_1940000 6369 . ct C 8 ABlow _DP=42;_AB=19 GT:AD 0/1:34,8 +11_1910000_1940000 6654 . g A 43 . _DP=43;_AB=100 GT:AD 1/1:0,43 +11_1910000_1940000 7873 . g A 45 . _DP=45;_AB=100 GT:AD 1/1:0,45 +11_1910000_1940000 8084 . t C 54 . _DP=54;_AB=100 GT:AD 1/1:0,54 +11_1910000_1940000 10894 . t G 40 . _DP=40;_AB=100 GT:AD 1/1:0,40 +11_1910000_1940000 12259 . a G 35 . _DP=35;_AB=100 GT:AD 1/1:0,35 +11_1910000_1940000 15695 . g A 36 . _DP=36;_AB=100 GT:AD 1/1:0,36 +11_1910000_1940000 16353 . ctt C 14 . _DP=14;_AB=100 GT:AD 1/1:0,14 +11_1910000_1940000 20714 . c T 24 . _DP=42;_AB=57 GT:AD 1/0:18,24 +11_1910000_1940000 24531 . t G 32 . _DP=32;_AB=100 GT:AD 1/1:0,32 +11_1910000_1940000 24546 . gt G 25 . _DP=25;_AB=100 GT:AD 1/1:0,25 +11_1910000_1940000 25710 . t TTG 17 . _DP=46;_AB=37 GT:AD 0/1:29,17 +11_1910000_1940000 25813 . c CTG,CTGTG 13 . _DP=33;_AB=70 GT:AD 1/0:10,13,10 +11_1910000_1940000 26084 . ctg C,CTGTGTG 17 . _DP=36;_AB=75 GT:AD 1/2:9,17,10 +11_1910000_1940000 26212 . g A 29 . _DP=55;_AB=53 GT:AD 1/0:26,29 +11_1910000_1940000 26370 . c CTG,CTGTGTG 12 . _DP=34;_AB=68 GT:AD 1/0:11,12,11 +11_1910000_1940000 26521 . a G 30 . _DP=30;_AB=100 GT:AD 1/1:0,30 +11_1910000_1940000 26713 . a G 32 . _DP=32;_AB=100 GT:AD 1/1:0,32 +11_1910000_1940000 27735 . tc T 41 . _DP=41;_AB=100 GT:AD 1/1:0,41 +11_1910000_1940000 28524 . c A 18 . _DP=38;_AB=47 GT:AD 0/1:20,18