Hi! Does anyone know any tool that allows to compare genotypes between two compressed vcf files (.vcf.gz)?
(Or any ideas how can I do it without decompressing?)
How do you want to compare them? - you can potentially just do it via BCFtools and / or indexed awk arrays, but please tell us what you want to do.
I want to confirm if the genotypes are the same in my original vcf file versus the same annotated file. I'm also not entirely sure if they both are sorted (which can be a potential comparison problem for some tools). I just want to check that I didn't lose information in the process.
(In a multisample file)
I see... I would do the following:
bcftools annotate -x ID -I
I solved it with bcftools sort - there's no need to uncompress to sort files - and then bcftools stats -v to compare between files
Great - thanks! I was not aware of BCFtools stats.