Petr Danecek

I don't understand the question completely. I can see how it'd be possible that N's in ALT column will not be matched well, but don't understand the part with "false"...

This would equal to listing all transcripts, wouldn't it, since everything what is not an exon is intron. I don't see the benefit, can you elaborate?

Most of the intronic sequence is shared between all or most transcripts, so I am reluctant to blow up the records like this unless the information is essential. I'll mark...

I wonder if the `GTisec` or `GTsubset` plugins would help. I did not write these so can't really tell.

I don't understand what you mean when say 'concatenate'. There are two tools to help with merging / concatenating, the `merge` command and the `concat` command. Please see the documentation...

This comes from the VCF parser in htslib when a value exceeds the maximum integer representable in 32 bits. It is a bit odd that this should happen for FORMAT/AO,...

Sure. You can just look in the original VCF and grep for position 160826 on chr8 and see what values there are for the FORMAT/AO field.

Can you also show full header please?

The tag names cannot contain the minus sign `-`, so the program does not attempt to interpret the whole string as a tag name. You may try to rename the...

@nicolaasuni do you want to take a look at your variantkey code? It appears it is not ready to handle missing ALT alleles