Petr Danecek

Thank you for opening these issues. The first is that sample subsetting in htslib does not reduce the BCF per-sample format size when the bulkiest samples are removed. I think...

Discussing this with others I propose the following solution: - add a new htslib API function to re-compress FORMAT fields with unused values at the end. This will allow to...

VCF format is not able to distinguish between a missing haploid genotype and a missing genotype with unknown ploidy. In BCF this is possible to distinguish between the first and...

This is a generic error propagated from inside htslib and occurs when the program attempts to write a VCF/BCF line with unresolved tags. In plain English: the input VCF most...

Can you please index with `bcftools index` instead and try again? If the problem persists, could you please provide a small test case, including your index? In my tests I...

Hmm, I don't think it should and can't think of a good reason where the bug would come from. Are there many haploid genotypes in the VCF? Any chance you...

I agree it would be a nice feature to have. One can obtain a list of sites for use with -R by running ``` bcftools query -f'%CHROM\t%POS\n' C.bcf | bgzip...

Err, can you please provide a small test case to reproduce the problem?

Since you are not showing any data, it is impossible to tell what went wrong. The issues you reference give some useful tips, not sure how to help more here.

Is it really mpileup or is sort?