Extracting regions with a specific coverage from sorted BAM files for multi sample comparison (uneven coverage)

Question

[Salmo]

Hello all.

I have created BAM files for 10 samples . My goal is to identify SNPs that are shared among samples (or by a subset of my sample) , as well as those that are sample-specific . Ultimately, I'd like to identify the genotype (haplotype) of each sample, and reconstruct their relationship.

The main issue I am having is that coverage is highly uneven among samples. For example, a region X may be covered in only 4 samples, while a region Z may be covered only in 3).

I am looking at extracting all regions that are covered (1X and over, or from 2X to 50X) in all samples (or a subset of samples), and then use these to call SNPs and extract genotypes.

Any help on this matter will be greatly appreciated. Thank you very much!

Best, Salmo