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CGI- VCF file

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

somatic vcf cgi

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updated 4.9 years ago by Ram

• written 12.3 years ago by kanwarjag

1 answer

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.

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updated 6.8 years ago by Ram

• written 12.3 years ago by Pablo

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