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seppinho / nft-vcf

nf-test plugin to provide support for VCF files.
MIT License
4 stars 1 forks source link

Uncompressed VCF variants #6

Open fellen31 opened 2 months ago

fellen31 commented 2 months ago

Hi,

Thanks for writing this plugin!

I'm having trouble using variants/variantsMD5 on uncompressed VCFs, header seems to work fine. Is it supported to be supported?

/Felix

seppinho commented 1 month ago

Correct, for some methods, we require a BGZF-compressed file (.vcf.gz) because we are using the query functionality of HTSJDK, which requires an index file. One approach could be to compress the VCF file using BGZIP and generate the index directly within the code. Would it also be possible for you to work directly with a .vcf.gz file?

fellen31 commented 1 month ago

I see, in this case I wanted to snapshot the output of a software that only supports uncompressed VCF output.

If you already generate the index, then perhaps it would be okay to also compress the VCF within the code?

seppinho commented 1 month ago

I understand. I'll do my best to implement this feature. If you feel like contributing to a PR, let me know!