Issues with bcftools
Hi, I can’t seem to solve this issue. I produced .gz versions of my .vcf files, and I indexed them, however bcftools merge does not seem to work any way I try. Example:
bcftools merge -l list.txt > merged.vcf
Produces:
Failed to open example.final_comp.vcf: unknown file type
Thank you for your help.
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Pierre Lindenbaum
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hgrsce •
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hgrsce •
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Could you try by giving the absolute paths to VCFs in your list.txt?
I tried that, also. The issue persists.
check example.final_comp.vcf is a non-empty valid VCF.
furthermore, VCF files must be compressed and indexed
It is not empty, and it's valid. I also compressed and indexed the files. The same issue still occurs.
show me output of the following command: