Filtering methods for samtools or GATK

[kardy]

Hello everyone!

I just started my PhD and my level of expertise is fairly low about bioinformatics! Is there any advice regarding different coverage levels? ( 10x vs 50x or more ).
I would need simple instructions for filtering using either samtools or GATK. We are looking for ROH (runs of homozygosity) so we need to avoid variants being called where they are not genuine. I tried to use MQ < 40 and DP>200 but not sure if they are right or fixed.

Thanks for your answer!

Kardy