How does bcftools isec do the intersection?

Question

[Hadi M]

Hi all,

I am just wondering how does bcftools isec do the intersection? Does it take account of other headers, e.g. REF and ALT, or it just look at the CHROM and POS and consider it as intersection despite the REF and ALT?

Thanks and cheers.

Answer 1

[finswimmer]

Hello Hadi M ,

bcftools isec takes CRHOM, POS, REF and ALT into account. But not the genotype.

fin swimmer

[dariober]

Hi- To add to your answer, maybe worth mentioning that with the option --collapse you can control what makes intersecting records compatible

[Hadi M]

Thanks for the answers both of you :) Cheers.