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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
365 stars 56 forks source link

Feature: read from stdin #67

Closed matthdsm closed 7 years ago

matthdsm commented 7 years ago

Hi Brent,

I don't know if this is technically possible, but how do you feel about enabling vcf input from STDIN? It would be nice to be able to pipe output from VEP straight to vcfanno, without having to save an intermediate file.

Cheers M

brentp commented 7 years ago

you can do this currently using /dev/stdin as the file handle. "-" might work as well.

matthdsm commented 7 years ago

oh, I wasn't aware this was already possible.

Thanks! M