Maybe I'm having a brain-freeze so excuse me if this is a waste of everyone's time...
I am working with an organism with ~700Mb genome.
I have bam files of two individuals that are whole genome sequenced with the average depth of ~150.
I would like to count the occurrences when both of the individuals are homozygote for the reference allele. Preferably without any hassle or space, I have no need to create a vcf file for the task or save the information in any form. Something like '
gatk or mpileup... argument that only retains sites when all are homozygote reference... delete tmp file...'. So the question is: what would be the "cheapest"/fastest way to count where these individuals are homozygote reference?
Come to think of it... I'm asking for a line count value on an "inverted variant file"/"gVCF minus variation"