Petr Danecek

You seem to be using some older version of the plugin? Even though the command line you are showing suggests that you are at the version 1.17, the code there...

We still need a test case to reproduce the problem, unable to proceed without it, sorry.

Thanks for the pull request. I am thinking if it should be made optional and if it would be useful to make into something more general. We already have average...

It seems you want the VAF annotation, variant allele frequency ``` FORMAT/VAF Number:A Type:Float .... The fraction of reads with the alternate allele, requires FORMAT/AD or ADF+ADR ``` If the...

What version of bcftools do you have? If it is the latest, would you be able to isolate the problem and create a minimal test case for us to reproduce?...

Uh, try with the latest version then and see if the problem persists http://samtools.github.io/bcftools/howtos/install.html

The error message suggests that the BCF is corrupted. Do commands like this work on the file? ``` bcftools index your.bcf bcftools view -Ou -o /dev/null your.bcf ``` command work...

I run multiple tests repeatedly to account for differences in the computing farm load and was able to confirm that `+fill-tags` is somewhat slower than `+fill-AN-AC` on a 470k sample...

That's a correct observation. Hopefully a different solution might work. As you've shown above, one of the key inputs of the algorithm are population allele frequencies. If the AF tag...

> Note: could not parse as PED: sample.txt It is not an error, only a warning (albeit admittedly a bit useless and confusing). Check if the GT fields have the...