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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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Tabular output from `cnv_facets` #51

Closed Faizal-Eeman closed 1 year ago

Faizal-Eeman commented 1 year ago

Hi @dariober,

It'd be nice to allow users to save the original output from FACETS in a tabular format rather than only having the output be in a VCF format. Can this be added as a new feature?

Faizal

dariober commented 1 year ago

Hi Faizal,

While saving the tabular output from facets should be an easy feature to add, I'm reluctant in doing so since more features mean more things to maintain and that can break later. You can convert VCF to tabular format fairly easily with bcftools query.

I'm going to close the issue but feel free to re-open or to ask more information on how to convert vcf to tabular (biostars.org may be a better place for this).