Petr Danecek

This can be from a number of reasons, impossible to tell when you don't show the commands you used nor the VCF you are trying this with. Most likely the...

Uh, this is calculated here https://github.com/samtools/bcftools/blob/develop/mcall.c#L578-L584 and should have been removed long time ago. It's a naive metric based on HWE assumption and should be replaced with https://github.com/samtools/bcftools/blob/develop/plugins/fill-tags.c#L500.

The program seems killed by your system, possibly because of low memory. Check what version of bcftools are you using. Does it work with fewer files? By the way, you...

Can you please provide a test case where this feature does not work with the current version of bcftools (incorrectly) but is fixed with this pull request? The added test...

Adding this could be quite straightforward by using vcfbuf_t with a new mode SORT_BY_ALLELE mode. This would make all output from `norm` sorted this way.

It would be good to see the full command line. Was the `-i` option used and the DP tag is not defined in the header as integer? I just pushed...

Well, you can look for examples online or in the VCF specification. Guessing what may be possibly wrong in your VCF is beyond the support we can provide. This is...

The problem is caused by the fact that chromosome names are not stored in the BCF body, only pointers to the header. Therefore the header cannot be changed without also...

Hmm, this is tricky. - if there was an intermediate VCF file, I'd run `reheader -f` on those before converting to BCF. I think the order in VCFs should be...

It is possible you encountered a bug. Can you please share the output and the `*.txt.gz` files to reproduce the problem? If it is sensitive data, can you send me...