This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Complete Genomic Vcf File

I was wondering is there any third part software which can allow me to filter and annotate VCF file from complete genomics in addition to CGA tools recomended by CG.

Thanks

vcf genomics
• 4,769 views • link
updated by Ram Ram • written by rob.costa1234 rob.costa1234

To annotate the variants, I normally use Annovar for our human data.

With regards to filtering, it really depends on what you want to do and what you want to know. Maybe if you provide some more details, we can provide tailored answers?

• 0 views • link
written by BruceB BruceB

Thanks for a quick reply. Complete genomics gave masterVarBeta and somaticVcfBeta files. My aim is to identify somatic mutations in cancer vs normal so would like to filter for dbSNPs and variations that are unique to cancer.

• 0 views • link
written by rob.costa1234 rob.costa1234

1 answer

I use SnpEff and SnpSift

• 596 views • link
written by Pavel Senin Pavel Senin

Log in to answer this question.

More posts like this