Filter pileup file for completeness

Question

[AP]

Hi all,

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!

Answer 1

[AP]

6 months later: simply filter your pileup file using a grep command, removing lines that have a relatively low coverage. For instance: grep -vw '[0-5]' A.mpileup > B.mpileup will remove all lines with coverage below 5.