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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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How to convert to standard vcf format to be used for downstream analyses? #32

Closed lipikakalson closed 9 months ago

lipikakalson commented 9 months ago

Hi, thanks for the amazing tool. I successfully ran the Scomatic pipeline, output I have is in .tsv format ( which somehow is looking like vcf format). But, how can I convert it into standard vcf format (as used by many other downstream analyses tools).

I tried to convert it using vcf2vcf.pl from vcftools, but no success.

Thanks, Lipika

Francesc-Muyas commented 9 months ago

Dear user,

We do not provide one functionality for getting a vcf format. However, in our manuscript, we have annotated these variants using Annovar. Please find in the FAQs section an easy way to do it.

Thanks, Fran