CGI- VCF file

Question

[kanwarjag]

I have performed whole genome seq with complete genomics. one of the out put file is VCF file of mutations calls between normal and tumor samples. I would like to filter and annotate this file. I was wondering if some one has worked with CGI VCF files on this forum and can share which may be the best utility to work with such files.

Thanks

Answer 1

[Pablo]

SnpEff and SnpSift work OK on CGI files (at least, it worked OK last time I tried CGI files).

Plus SnpEff supports germline-somatic comparisons of cancer samples.

CGI tends to have a relatively high false positives of mixed variants (InDels + MNPs), which might be a problem.