AF and MLEAF calculation

mehar

Hi all,

Could someone explain how the values for the fields AF and MLEAF are calculated in the vcf output?

Geraldine_VdAuwera

Hi there,

Have you looked at this thread?

http://gatkforums.broadinstitute.org/discussion/1283/mleaf-and-mleac

mehar

Thanks. It answers to some extent.

How is the AF calculated? Is it the ratio of the alternate allele to the total alleles (alt/ref+alt) ? And in case of multisample calling it reports a single value for AF. How is to possible to know the AF for individual sample?

Geraldine_VdAuwera

For AF you should look at the VCF specification. MLEAF is a variation of AF, it is defined in the header of the VCF and computed from the EXACT model (see exact model math for details).