Petr Danecek
Petr Danecek
Please update to the latest, 1.21, then `-c ...,-ID,...` should work.
There is a way to do it, but it involves multiple steps. One can annotate failing samples prior to merging the VCFs, first extract the failing sites with `bcftools query`,...
If the files are indexed, then yes, it should work. If it does not, you'll need to provide more details, for example the error message printed by the program...
Mm, I don't understand the terminology you are using (for example what do you mean by "de-replication", "re-expansion", the reference to USEARCH, etc) and don't know if you are referring...
What is the version of bcftools you are using? I just tested with the latest and it seems to be working as expected.
We are at version of bcftools 1.21, please update http://samtools.github.io/bcftools/howtos/install.html
To cross-reference, this seems to be a duplicate of https://github.com/samtools/bcftools/issues/1923#issuecomment-2118679724. Since the example does not show the reference sequence, I can only make a few general comments. Variant calling is...
These variants are not overlapping. For example, the insertion in the first example inserts A between the positions 28728 and 28729.
It's exactly the same case. The first happens between 30586 and 30587, 30588 is not affected by the insertion.
I can imagine this, probably best done at htslib level and maybe controlled by an environment variable.