Petr Danecek

Hopefully the new version of the plugin, `+mendelian2`, resolves this issue. See also https://github.com/samtools/bcftools/issues/1738#issuecomment-1298518068

Yes, thank you, this is a good workaround. (Though different from the request of making this part of the -R functionality.)

The program calls SNVs independently and reports MNPs in separate records, so this is not a bug. Unfortunately, we do not have a tool in bcftools yet that would join...

It would be helpful to have a small test case to reproduce the problem and improve the code. In the meantime, this branch has a new mpileup option --indels-2.0 which...

OK, I checked and can confirm that the read counts are not correct with any version. I'll add this to the test suite to investigate later. By the way, it's...

Thanks for the issue, however, it does not give enough information, not sure how to help! One common problem is the chromosome naming (`chr1` vs `1`), which needs to be...

It is possible, just subset by sample as if you'd do in a filtering expression. For example, to compute the value across the first three samples, run as ``` bcftools...

Uh, I see. That is not possible I am afraid with a single command right now, the `-i` option is currently not taken into account here

We'd need a small test case to debug this, unfortunately can't help just from the screenshot.

Please provide a small test case (VCF) to reproduce the problem and make sure you are using the latest version of bcftools.