Major Minor

Inferring Major and Minor alleles

arguments

-doMajorMinor [int]=0

The inference method is chosen based on the data input.

From alignment data

If you input sequencing data like the bam format you can choose to infer the major and minor allele by picking the two most frequently observed bases across individuals. This is the approach from here: citation. To use this appraoch choose

-doMajorMinor 2
-doCount 1

From genotype likelihood data

From input for either sequencing data like bam files or from genotype likelihood data like glfv3 the major and minor allele can be inferred directly from likelihoods. We use a maximum likelihood approach to choose the major and minor alleles. Details can be found here Citation. To use this appraoch choose

-doMajorMinor 1

From genotype probability data

Currently only genotype probability data in beagle output format is allowed. This format already contains information for the major and minor allele.