Petr Danecek

First fix the VCF header and we can start from there. Also a test case, i.e. a small VCF including its header, is required to investigate this further.

The recommended workflow is described here http://samtools.github.io/bcftools/howtos/variant-calling.html The command in its simplest form looks like this ```` bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf...

A simple and quick hack for now is to modify `test.pl` to round float values first before comparing.

Thinking about it more, this is actually the right place to do it. The program works correctly, these rounding problems are just an artifact of evaluation. The rounding would be...

Can you try with this latest commit please? I expect some of the failures might be fixed by this. For the rest, it would be helpful to see all the...

It is possible that indel AD counts will be improved in this pull request https://github.com/samtools/bcftools/pull/1679

That's correct. The pull request will be integrated into develop, but may take a while.

The output is not described properly anywhere, the idea was to make it self-explanatory, more or less. ``` - sample - non-reference discordance rate .. the explanation is elsewhere in...

Please read the VCF specification here http://samtools.github.io/hts-specs/VCFv4.3.pdf Regarding filtering with bcftools, you can use the `-i/-e` options.

There is a brief description in the header, but it is a good point this should be documented more. I am reopening the issue and labeling appropriately.