Issues with bcftools

Question

[hgrsce]

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.

[barslmn]

Could you try by giving the absolute paths to VCFs in your list.txt?

[hgrsce]

I tried that, also. The issue persists.

[Pierre Lindenbaum]

check example.final_comp.vcf is a non-empty valid VCF.

furthermore, VCF files must be compressed and indexed

[hgrsce]

It is not empty, and it's valid. I also compressed and indexed the files. The same issue still occurs.

[Pierre Lindenbaum]

show me output of the following command:

cat list.txt | while read F; do file "${F}" && bcftools view "${F}" > /dev/null; done