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calculating sigma for Depth of Coverage cutoffs

sagipolanisagipolani Member Posts: 41

Hi,

I would like to filter variants based on max DP. I understand that in order to define the max DP cutoof there is a need to calculate the Sigma, as stated in GATK's best practices:

"The maximum DP (depth) filter only applies to whole genome data, where the probability of a site having exactly N reads given an average coverage of M is a well-behaved function. First principles suggest this should be a binomial sampling but in practice it is more a Gaussian distribution. Regardless, the DP threshold should be set a 5 or 6 sigma from the mean coverage across all samples, so that the DP > X threshold eliminates sites with excessive coverage caused by alignment artifacts."

Hence, how can one calculate the sigma, and what is it exactly?

Thanks!

Sagi

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Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,428 admin
    Accepted Answer

    That sounds right to me. As always, make sure to examine your results carefully to make sure that this cutoff is appropriate for your data.

    Geraldine Van der Auwera, PhD

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