Petr Danecek
Petr Danecek
Any chance you could provide a concrete test case? Since you are quoting LAD, it is not clear what exactly the input data is like. > Also, is there an...
@chundruv There is a problem with the input VCF: the tag LAA is defined as `Type=String` but it must be defined as `Type=Integer`. I just pushed a commit which prints...
@IdoBar The problem is that the VCF has haploid genotypes: the `binom(AD)` function selects the input values based on the GT tag, so in this case it has nothing to...
As described in the documentation, the function can take one argument (`binom(FMT/AD)`) and in that case the indices of values to use are determined from GT. Or one can define...
AD is defined as `Number=R`, there can be more than two values. That's why GT step is required.
I believe this is resolved now, please shout if not.
It's possible you encountered a bug: - Can you try with the latest github version please? - If the problem persists, can you test if it's just slow, or it...
While experimenting, can you also try `--indels-2.0`, if that makes any difference in speed...
Is it possible to share a small anonymized BAM slice for debugging?
This looks similar to https://github.com/samtools/bcftools/issues/2297; which version of bcftools are you running?