gffread - heterozygotes and indels

[Axel]

Hi all,

I am trying to get .fasta files for each CDS in a .gtf file and the most obvious way I can find of doing it is to use gffread and the target genome. However, I am wondering if anyone knows how gffread deals with heterozygotes. For SNPs I assume it uses the IUPAC ambiguity codes which is fine by me, but what about heterozygous indels? I don't have many of them in my genome but I like knowing what the tools I'm using actually do rather than just treating them as a magical black box.

Cheers

[TiborNagy]

AFAIK gffread does not deals with heterozygotes.

[Axel]

Thanks TiborNagy. Do you know what the behavior is if it encounters a heterozygote? what will it output into the fasta sequence?