Hello!
I'm wondering if it's possible to create a consensus sequence that combines the data of BAM/SAM files and filtered VCF files so that areas of low coverage could also be masked? My intention is to do a sliding window analysis of some population genetic parameteres (Nei's pi, Watterson's theta etc.). Something like GATK FastaAlternateReferenceMaker looks promising, but the problem is that areas of low coverage (<7) must be absent from the consensus.
I'm wondering if it's possible to create a consensus sequence that combines the data of BAM/SAM files and filtered VCF files so that areas of low coverage could also be masked? My intention is to do a sliding window analysis of some population genetic parameteres (Nei's pi, Watterson's theta etc.). Something like GATK FastaAlternateReferenceMaker looks promising, but the problem is that areas of low coverage (<7) must be absent from the consensus.