I am trying to filter a SNP file (.vcf) for max depth. Instead of choosing a random number it has been suggested that I could use the
mean + (2*SD) as a limit for the amount of depth allowed.
Does anyone know how to carry this out using
vcftools or the alike?
I know I can filter using
-max-meanDP etc. but how would I apply the calculation instead?
I saw this question but I also get the wrong answer (outputs 0 0). It is also very old so thought it would be best to start another.
Thank you for your help in advance.