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2 hours ago by

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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