Petr Danecek

@freeseek I don't know much about variantkey and how it should handle sites with no ALT allele. Is it acceptable to just skip the ref-only sites?

OK, I did it this way, hope it will work. Thanks

I am not sure what's causing this, the error comes deep from inside matplotlib. Any matplolib experts out there?

Try to add square brackets before the suffix: `\includegraphics[width=15cm]{{indels.0}.pdf}`

This was addressed in the new `+mendelian2` plugin. Please take a look and if anything is not to your liking, please report as soon as possible. For example, the output...

No, this is not in a versioned release yet and we do not maintain conda packages ourselves. You'll need to compile from source. But that is not difficult http://samtools.github.io/bcftools/howtos/install.html

@gabeng Indels may be missed because of high depth, try increasing -L ``` -L, --max-idepth INT Maximum per-file depth for INDEL calling [250] ```

Really? I am using the latest github version on the develop branch and this is what I am observing with your data: ``` $ bcftools mpileup -f hs37d5.fa test.bam -r...

I see it now, thanks for the test case. This should be fixed by https://github.com/samtools/bcftools/commit/815fd54e261ee400010082129ff860ff7023c5d0. By the way, please open a separate issue next time and reference a related issue...

Normalization is a separate step, yes, just stream through `bcftools norm`. Regarding the difference, maybe the 1.16 version just inserted a missing site via the -i option that it could...