Problems defining ploidy with bcftools call

[amankowski]

Hello,

I am trying to run a combination of bcftools pileup and call, defining --ploidy 1. This however fails.

Command:
bcftools mpileup -a AD,DP,SP -Ou -f ${ref}.fasta ./${lib}.bam | bcftools call -f GQ,GP -cO z -o ${lib}.vcf.gz --ploidy 1
Error:
[mpileup] 1 samples in 1 input files
Failed to open -: unknown file type

During the first run, I didn't specify --ploidy and it ran through as expected.

Any help is highly appreciated.
Thanks a lot!
Anna

[pd3]

Mmm, it does not seem like a problem with the --ploidy option. The error message suggests that the call command did not receive a valid BCF on input. The best way to check is to run the two commands sequentially

bcftools mpileup ... -Ou -o step1.bcf
bcftools call ... step1.bcf -o output.bcf

In case the problem really is with the --ploidy option, can you provide a small test case to reproduce the problem?