Petr Danecek

The file `sample.txt` you showed above is not a PED file. For the format definition see for example here https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format Regardless, if the ploidy is not determined and output correctly...

You are not showing how INFO/AS_MQRankSum is defined in the header, but the error message is clear: the program expects three values but found only one. Since at that position...

I am open to this feature, but must warn it will need some careful thought. The annotation file can be a tab-delimited file or a VCF/BCF, which means there are...

Hello, I was wondering if there was any progress or more thoughts on this? I am repeatedly facing the same problem, the embedded jpeg just looks better and I am...

I still dream about this function at nights. Would it be very hard to implement? I would be happy to help...

I can imagine writing an algorithm that creates a mapping between two color spaces - from darktable's interpretation of raw file to whatever we observe in the embedded jpg. However,...

Just to make sure: when you say "good luck fitting that into the scene-referred workflow of darktable", do you mean you think it would be difficult? I have no knowledge...

@sg456 I will send you a file offline. Can you contact me by email? The address is on my profile page.

When the `-A` option is added and `-v` is not used, this tells the `call` command to keep all sites, including non-variant sites, and to keep all observed alleles in...

Any chance you could provide a small test case to reproduce the problem? It is concerning that `bcftools mpileup` should produce a VCF that cannot be parsed by `bcftools call`...