Petr Danecek
Petr Danecek
1. this is a check if all REF/ALT alleles in the VCF are compatible with either TOP or BOT notation: the values mean "true" (1) or "false" (0) 2. I...
@bgb-ipl Obviously, for a file to be TOP or BOT compatible, all its sites have to be compatible with one of the conventions. @maegsul This is useful. Knowing which of...
Hi, apologies for the delay. I am happy to add a support for this. However, I'd need real world data for testing because it's tricky to get the ambiguous `G/C`...
I meant the manifest feature suggested by @maegsul.
No, it was not. A good test case would be required to even start thinking about it
Uh, out of curiosity, how much space are you gaining by compressing bams with gzip? It must be by a negligible amount, as bams are already bgzip-compressed. If the size...
Which version of bcftools are you running? The notation `~POS` was deprecated in favor of `-POS` in the latest version 1.21.
This is the expected behavior for now, the program is not smart enough to join the two records split across different positions. The inverse of `bcftools norm --atomize` is needed...
You can check the output of the `mpileup` step to see if your read filtering is not too strict, the AD tag shows the number of reads that were included...
The number of markers would be the number of sites in the VCF that contributed to making the decision in that region.