Petr Danecek
Petr Danecek
> I'd argue otherwise. The spec explicitly states a non-call must have GT ./. (presumably only if written out). It doesn't explicitly forbid GQ, but the GT bit is also...
Hi, sorry I am a bit late to this thread, or maybe I was on it too early, depending on how you look at it The ideas proposed in the...
> I do have confusion over LGT vs GT though. If we're using LAA instead of LA, then LGT doesn't make sense because a GT `0/1` would refer to what...
> @pd3, I’d like to make a final nudge on LGT, but after this I’ll be quiet about it. > > I agree with your points one and two: LGT...
> For merging and splitting local representations it will be necessary to specify the expected number of elements in local array shaped fields. Using “.” will not achieve this. Using...
How do you distinguish the duplications, by their ID? Would `--merge id` work in such case?
I don't think this is required, the program should respect whatever is in the VCF, GFF and Fasta file. If it's not working with your data, please provide a small...
I suspect some of the input VCF is broken in some way and while the earlier versions silently ignore it, returns an error, as clearly indicated by the error message...
@wangmingcheng as stated above, any chance you could provide a small test case to reproduce the problem? It is not possible to help without being able to reproduce the problem...
This could happen when existing INFO/AC,AN counts are different from the ones calculated from the genotypes FORMAT/GT. The command `bcftools view -S` recalculates the values. If this is not the...