Mercurial > repos > iuc > bcftools_annotate
diff test-data/csq.vcf @ 5:eb782a60fc53 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
| author | iuc |
|---|---|
| date | Thu, 13 Apr 2017 17:44:38 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csq.vcf Thu Apr 13 17:44:38 2017 -0400 @@ -0,0 +1,40 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence"> +##contig=<ID=1,length=2147483647> +##contig=<ID=2,length=2147483647> +##contig=<ID=3,length=2147483647> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SmplAAA SmplBBB +1 90 . C T . . EXP=5_prime_utr|XYZ|ENST00000000001|protein_coding GT 1|0 1|1 +1 102 . C T 1 . EXP=synonymous|XYZ|ENST00000000001|protein_coding|+|1Y|102C>T GT 1|0 1|0 +1 103 . G A 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2I|103G>A GT 1|0 0|0 +1 103 . G C 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2L|103G>C GT 0|0 1|0 +1 107 . G A 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|3R>3Q|107G>A+108T>A GT 1|0 1|0 +1 108 . T A 1 . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@107 GT 1|0 1|0 +1 121 . ACG A . . EXP=inframe_deletion|XYZ|ENST00000000001|protein_coding|+|5TY>5I|121ACG>A+124TA>T,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 1|0 +1 124 . TA T . . EXP=@121 GT 1|0 1|0 +1 128 . T C 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|7V>6A|128T>C+129A>C,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0/0 +1 129 . A C 1 . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@128 GT 1|0 0/0 +1 140 . TA AACG . . EXP=inframe_insertion|XYZ|ENST00000000001|protein_coding|+|8LR>7QRR|140TA>AACG+142C>CC,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0|0 +1 142 . C CC . . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@140 GT 1|0 0|0 +1 145 . AC TA . . EXP=stop_gained|XYZ|ENST00000000001|protein_coding|+|10T>10*|145AC>TA GT 1|0 0|0 +1 160 . TA T . . EXP=*frameshift|XYZ|ENST00000000001|protein_coding|+|12YVRT>12SYV|160TA>T,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0|0 +1 190 . C T . . EXP=3_prime_utr|XYZ|ENST00000000001|protein_coding GT 1|0 0|0 +2 97 . A C . . EXP=3_prime_utr|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +2 105 . AC A . . EXP=@121 GT 1|0 0|0 +2 121 . AC A . . EXP=frameshift|ABC|ENST00000000002|protein_coding|-|11VVRTY>11*|105AC>A+121AC>A,splice_region|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +2 126 . C CTT . . EXP=@127 GT 1|0 0|0 +2 127 . G GG . . EXP=inframe_insertion|ABC|ENST00000000002|protein_coding|-|9T>8TK|126C>CTT+127G>GG GT 1|0 0|0 +2 144 . TAC T . . EXP=@148 GT 1|0 0|0 +2 148 . TA T . . EXP=inframe_deletion|ABC|ENST00000000002|protein_coding|-|5YV>5T|144TAC>T+148TA>T,splice_region|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +2 164 . T G . . EXP=missense|ABC|ENST00000000002|protein_coding|-|3T>3P|164T>G GT 1|0 0|0 +2 165 . A C . . EXP=synonymous|ABC|ENST00000000002|protein_coding|-|2R|165A>C GT 1|0 0|0 +2 169 . A G . . EXP=@170 GT 1|0 0|0 +2 170 . C T . . EXP=missense|ABC|ENST00000000002|protein_coding|-|1V>1T|169A>G+170C>T GT 1|0 0|0 +2 199 . G T . . EXP=5_prime_utr|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +3 20 . T A . . EXP=non_coding|mir-007||lincRNA GT 1|0 0|0 +3 109 . ACGTACGT A 1 . EXP=splice_acceptor|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0 +3 113 . A T . . EXP=splice_region|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0 +3 120 . T A . . EXP=intron|QWRTY||protein_coding GT 1|0 0|0 +3 152 . T A . . EXP=splice_region|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0 +3 159 . G A . . EXP=splice_donor|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0