Is there a straightforward way to filter a pileup file for completeness using samtools (or other programs)? I would like to exclude sites based on the proportion of missing data (e.g. SNP present in 80% of the samples). Basically, I want to do the same than what vcftools --maxmissing does but on a pileup file instead of a VCF file.
Any help would be greatly appreciated! Thanks!