Petr Danecek

This is a side effect of the way the dictionary is coded in HTSlib, which was the first implementation of BCF. The IDX feature that allows to drop tags from...

Not exactly a naive hack like that. The code that later became HTSlib was developed first and unofficially more or less defined what BCF format looks like. In the original...

@jkbonfield - re 2. From the logic of the dictionary, a dtictionary-defining record for tag `X` is the first record that defines the string `X`, be it FILTER, INFO, or...

Even if PASS does not appear in the body, it still must be implicitly defined by the dictionary, otherwise on the first encounter of a filter one wouldn't be able...

Can you please try if the commit I just pushed fixes the issue? I could reproduce the problem only partially, the commit fixes the malformed INFO tag. However, I was...

@jkbonfield This bug is probably related to https://github.com/samtools/bcftools/issues/665?

MNPs and other complex events can be now decomposed using the new `norm -a` option. Note that although the code correctly transfers annotations into split records respecting the various Number=R,G,A...

Try to run mpileup with `-B`. Also, any chance you could share a slice of the bam to reproduce the problem locally?

Thank you for sharing the data offline. Unfortunately, this is one of the cases that show limitations of `mpileup` which operates well in nice regions but has problems in places...

The option c) is problematic because indels will create ambiguities and the VCF merging step will produce very fragmented results. Option a) will create a big overhead from many files...