Petr Danecek
Petr Danecek
I am unable to reproduce the problem. Can you provide a small test case? This works just fine for me ``` $ mkdir xx $ chmod -rxw xx $ bcftools...
It seems the problem is not with permissions but with something else. Any chance you could share a small test case to reproduce the problem?
I don't understand the issue, can you provide more details. From your description it is not clear which bcftools command you are unhappy with and how were the two VCFs...
I am not opposed to adding this feature, but it is unlikely to happen by my doing. What is the motivation for this request? VCF specification does not mandate any...
Can you share the GFF, or part of it, and show the command you are using please?
Can you make available the entire GFF file, not just the snippet?
We need a small test case to reproduce the problem. The command itself looks ok
That's bad phrasing, it's the same thing, the option has been renamed in that command, so even when some allowed words can be missing in one or the other, those...
What you want is the inverse of the --atomize operation. This has not been implemented yet. Duplicate of https://github.com/samtools/bcftools/issues/2438#issuecomment-3102803133
It merges lines with the same position into a multiallelic site. It is not the same as merging, say, two SNPs into one MNP