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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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bcftools csq: Change chromosome name requirement. #2294

Open niederhuth opened 1 month ago

niederhuth commented 1 month ago

Could you please drop the requirement that chromosome start with "chr" from bcftools csq. This creates many headaches when working with other species where this is not the case.

pd3 commented 1 month ago

I don't think this is required, the program should respect whatever is in the VCF, GFF and Fasta file. If it's not working with your data, please provide a small test case to reproduce the problem. Also, make sure you are using the latest version, there were some improvements in the code to work around situations when the three input files used different conventions.