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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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slivar tsv: change --csq output delimiter for csq columns #109

Closed zihhuafang closed 2 years ago

zihhuafang commented 2 years ago

Hi @brentp:

Is it possible to change slivar tsv --csq output delimiter for the CSQ columns? Currently, the aggregated info (one column) from CSQ fileds is "/" separated. I would like to export the CSQ fields with another delimiter.

Thanks in advance. Zih-Hua

brentp commented 2 years ago

Hi, sorry for the delay, I missed this. It's currently not possible. I think it's simple enough to post-process the tsv output to change that, rather than adding complexity to slivar, what do you think?

zihhuafang commented 2 years ago

Hi Brent,

I do agree that post-process tsv is feasible, which is what I am doing now. It's not a necessary feature for sure.

Just that it is a lot of grouping and cleaning of the dataframe due to delimiter. One example would be exon number (e.g. 3/10) or amino acid change (R/V) from VEP, which use '/' as well. I need to group by missense, synonymous and UTR variants and organise the split csq_column accordingly. Nevertheless, it's not something that the end-user can't handle.

Thanks for the thought!