Mercurial > repos > nml > filter_density
diff test-data/1.vcf @ 0:c27b4346352f draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
| author | nml |
|---|---|
| date | Tue, 27 Aug 2019 12:30:47 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.vcf Tue Aug 27 12:30:47 2019 -0400 @@ -0,0 +1,38 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth"> +##contig=<ID=1,length=2147483647> +##contig=<ID=2,length=2147483647> +##contig=<ID=3,length=2147483647> +##contig=<ID=4,length=2147483647> +##contig=<ID=5,length=2147483647> +##contig=<ID=20,length=2147483647> +##FILTER=<ID=Test,Description="Test filter"> +##INFO=<ID=DP2,Number=2,Type=Integer,Description="Depth"> +##FORMAT=<ID=DP2,Number=2,Type=Integer,Description="Depth"> +##contig=<ID=12,length=123456789> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AAA0001 BBB0002 +2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 +2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 +2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 +20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 +20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 +20 5 . TGGG TAC,TG,TGGGG,AC . PASS INDEL;AN=4;AC=2,2,0,0 GT:PL:DP 1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1 1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1 +20 59 . AG . 999 PASS AN=4 GT:PL:DP 0/0:0:4 0/0:0:4 +20 80 . CACAG CACAT 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13 +20 81 . A C 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13 +20 95 . TCACCG ACACCG 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13 +20 95 . TCACCG AAAAAA 999 Test AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13 +20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2,2 GT:PL:DP 1/2:0,3,5,3,5,5:1 1/2:0,3,5,3,5,5:1 +20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 +20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 +3 10 . GTGGAC GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 +3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 +4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 +5 22 . A AGA 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0