Major Minor

We allow the major and minor to be determined from either the counts of nucleotides, based on genotype likelihoods, specified by the ancestral/reference or even force both major minor to specific bases, which can be useful if you compare with HapMap data etc.

NB if you force a major -doMajorMinor 4 or 5 but this allele is neither the estimated major or minor, the site will be discarded.

Brief Overview

./angsd -doMajorMinor 
Command:
/home/software/angsd/angsd0.583/angsd -doMajorMinor 
	-> angsd version: 0.580	 build(Feb 26 2014 11:19:53)
	-> Analysis helpbox/synopsis information:
-------------------
analysisMajorMinor.cpp:
	-doMajorMinor	0
	1: Infer major and minor from GL
	2: Infer major and minor from allele counts
	3: use major and minor from a file (requires -sites file.txt)
	4: Use reference allele as major (requires -ref)
	5: Use ancestral allele as major (requires -anc)

Details

From genotype likelihood data

-doMajorMinor 1

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 of the method can be found in the theory section of this page and for citation use this publication Skotte2012 and is briefly described here.

From counts of data

-doMajorMinor 2

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.

Pre specified Major and Minor

Using the -sites option the major and minor allele can be predefined for the desired sites. The is very useful when comparing with other data sources e.g. SNP chips where the major and minor allele is known.

Forcing Major/minor

You can force the major and minor according to your reference or ancestral states if you have defined those -ref/-anc. We first estimate the major/minor from the data using -doMajorMinor 1/-doMajorMinor 2, and swap these accordingly with the major we are trying to force. If that is not the case the site will be discarded from downstream analysis.