Petr Danecek
Petr Danecek
Unfortunately, this is not sufficient, we need the fasta reference and the input VCF file.
Can you provide a small test case to reproduce the problem? Things you can check yourself: - which version of bcftools are you using? Does it fail also with the...
Short answer is no, we don't have a plugin designed to do that. Possibly `+fill-tags` could be used for that. Can you explain how are the DS vs HDS values...
What program was used to generate the VCF?
Can you please provide a small test case to reproduce both problems? Ideally, can you open a new issue for the other one, as it is unrelated to this one?
Mmm, it does not seem like a problem with the --ploidy option. The error message suggests that the `call` command did not receive a valid BCF on input. The best...
The problem is somewhat confusing as it is stated: you say you want to filter in intergenic regions but the example you gave seems unrelated. Instead, it seems the variant...
The question seems focused on the variant being intergenic. I am sorry but I still don't understand what is not working for you exactly. Can you provide a small test...
I think that should be possible using the reverse logic of `-e`, for example ``` bcftools filter -e 'COUNT(AD[0:*]) != 2' ```
For splitting into regions for this purpose it is best to run with `--regions-overlap pos` or `--targets-overlap pos`, see http://samtools.github.io/bcftools/bcftools.html#common_options Otherwise `bcftools norm` has the `-w, --site-win INT` option and...