gvcf output in BisSNP?

[Albert Vilella]

Dears,

I am testing BisSNP on a range of WGBS files, average 30x but some of them up to 120x.

I want to do variant and methylation calling, and ideally test the output vcf variant calls against Illumina Platinum Genomes 8.0 and NIST.

Is it possible to produce gcvf output so that the output vcf can be fully assessed against PG8?

https://www.broadinstitute.org/gatk/guide/article?id=4017

Thanks in advance,

Albert Vilella

Bioinformatics

Cambridge Epigenetix

Jonas Webb Building

Babraham Research Campus

Cambridge

CB22 3AT

www.cambridge-epigenetix.com