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Could someone explain how the values for the fields AF and MLEAF are calculated in the vcf output?
Have you looked at this thread?
Geraldine Van der Auwera, PhD
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?
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).