I have mapped reads to a reference genome of a related species. I want to remove reads which map to a specific region (chromosome) of the reference, but I don't know what the best way to go about it is. I'm doing variant calling, and I've been using the -t ^ option in bcftools call to exclude the relevant chromosomes, but does this target regions in the reference, or in the mapped reads? Is it the same thing? Is it better to do this during mpileup phase?
I feel completely lost and would appreciate an ELI5.