Filter SNPs for DP using mean + 2*SD
Hello all,
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 -minDP -maxDP -min-meanDP -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.
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One issue with that strategy is that the calculation may be biased. You may be detecting more variants at low frequencies, so your mean may be artificially low.
I see, but this would be controlled for by filtering using
-minDP?If not - how would you set the maximum depth allowance - so its not just an arbitary number? Thank you for your advice