Complete Genomic Vcf File

Question

[rob.costa1234]

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

[Ashutosh Pandey]

Similar posts: annotate a VCF file

Another tool: GEMINI: integrative exploration of genetic variation and genome annotations This one is from Quinlan group.

[BruceB]

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?

[rob.costa1234]

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.

Answer 1

[Pavel Senin]

I use SnpEff and SnpSift