CNV .vcf retrieve involved genes

Question

[cocchi.e89]

I have some CNV .vcf files generated through GATK Germline CNV pipeline, and I'd like to get the genes involved in each CNV.

Here an example of the VCF file:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  A13665
chr1    821001  CNV_chr1_821001_1632000 N   .   3076.53 .   END=1632000 GT:CN:NP:QA:QS:QSE:QSS  0:2:405:60:3077:118:91
chr1    1665001 CNV_chr1_1665001_1684000    N   <DUP>   46.24   .   END=1684000 GT:CN:NP:QA:QS:QSE:QSS  1:4:3:46:46:52:46
chr1    1753001 CNV_chr1_1753001_12901000   N   .   3076.53 .   END=12901000    GT:CN:NP:QA:QS:QSE:QSS  0:2:6170:24:3077:8:76
chr1    12902001    CNV_chr1_12902001_12904000  N   <DEL>   15.98   .   END=12904000    GT:CN:NP:QA:QS:QSE:QSS  1:1:2:8:16:6:8
chr1    12904001    CNV_chr1_12904001_12905000  N   <DEL>   63.67   .   END=12905000    GT:CN:NP:QA:QS:QSE:QSS  1:0:1:64:64:64:64
chr1    12905001    CNV_chr1_12905001_12913000  N   .   118.99  .   END=12913000    GT:CN:NP:QA:QS:QSE:QSS  0:2:7:3:119:17:49
chr1    12913001    CNV_chr1_12913001_12920000  N   <DEL>   121.20  .   END=12920000    GT:CN:NP:QA:QS:QSE:QSS  1:0:4:24:121:24:62
chr1    12921001    CNV_chr1_12921001_12922000  N   .   2.97    .   END=12922000    GT:CN:NP:QA:QS:QSE:QSS  0:2:1:3:3:3:3
chr1    12922001    CNV_chr1_12922001_12924000  N   <DEL>   200.18  .   END=12924000    GT:CN:NP:QA:QS:QSE:QSS  1:0:2:104:200:131:104
chr1    12924001    CNV_chr1_12924001_12930000  N   <DEL>   87.60   .   END=12930000    GT:CN:NP:QA:QS:QSE:QSS  1:1:4:5:88:15:52

I guess there may be some tools out there to do something similar, but I could not find anything.

Thank you in advance for any help!

Answer 1

[Pierre Lindenbaum]

annotate with VEP : http://www.ensembl.info/2020/03/27/cool-stuff-the-ensembl-vep-can-do-annotating-structural-variants/