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ikalatskaya / ISOWN

Apache License 2.0
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dependencies file missing #17

Open Hammermann opened 5 years ago

Hammermann commented 5 years ago

Dear Q the link to dependencies file is broken. I am having problems which the annotations from the annovar (function and exonic functions) are not added to the out put file. I was wondering may be it is because my annovar version is newer than 2012 one.

Hammermann commented 5 years ago

I actually narrowed it down to the addAnnovarToVCF.pl script. lets say I have this vcf file

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR

chr1 876499 rs4372192_876499 A G . PASS GERMLINE;SNP;AF=1.00,1.00;MQ=60;DB;1000G;[SureSelectHumanAllExonV4=1,1,[chr1,876429,876641]] AD:GT:DP:DP4 0,73:1/1:73:0,0,43,30 chr1 877715 rs6605066_877715 C G . PASS GERMLINE;SNP;AF=1.00,1.00;MQ=60;DB;1000G;[SureSelectHumanAllExonV4=1,1,[chr1,877537,878481]] AD:GT:DP:DP4 0,40:1/1:40:0,0,13,27

and this variant_function file intronic SAMD11 chr1 876499 876499 A G 1 . 73 chr1 876499 rs4372192_876499 A G . PASS GERMLINE;SNP;AF=1.00,1.00;MQ=60;DB;1000G;[SureSelectHumanAllExonV4=1,1,[chr1,876429,876641]] AD:GT:DP:DP4 0,73:1/1:73:0,0,43,30 intronic SAMD11 chr1 877715 877715 C G 1 . 40 chr1 877715 rs6605066_877715 C G . PASS GERMLINE;SNP;AF=1.00,1.00;MQ=60;DB;1000G;[SureSelectHumanAllExonV4=1,1,[chr1,877537,878481]] AD:GT:DP:DP4 0,40:1/1:40:0,0,13,27

and this exonic_variant function file line3 nonsynonymous SNV SAMD11:NM_152486:exon10:c.T1027C:p.W343R chr1 877831 877831 T C 1 . 24 chr1 877831 rs6672356_877831 T C . PASS GERMLINE;SNP;AF=1.00,1.00;MQ=60;DB;1000G;[SureSelectHumanAllExonV4=1,1,[chr1,877537,878481]] AD:GT:DP:DP4 0,24:1/1:24:0,0,2,22 line8 synonymous SNV NOC2L:NM_015658:exon9:c.A918G:p.E306E chr1 888639 888639 T C 1 . 70 chr1 888639 rs3748596_888639 T C . PASS GERMLINE;SNP;AF=1.00,1.00;MQ=54;DB;1000G;[SureSelectHumanAllExonV4=1,1,[chr1,888586,888756]] AD:GT:DP:DP4 0,70:1/1:70:0,0,37,33

but still my output looks exactly like the input vcf file.

qtrinh commented 5 years ago

Thanks. This is probably some format changes that we need to consider. We will look into this shortly.

Q

Hammermann commented 5 years ago

thanks a lot for the answer. it would be great if you could share some lines of the final annotated vcf

(isown.pl input) so that I could also try to reproduce it. Best

Hammermann commented 5 years ago

Hi just wanted to ask if you could have time to integrate the new Annovar?