Document ANGSD VCF allele convention

[thierrygosselin]

Summary

ANGSD’s VCF/BCF output uses the inferred major and minor alleles for genotype-likelihood and genotype-probability ordering. This can be confusing because the major allele may be written as VCF REF, rather than the reference-genome allele.

This documentation clarifies that:

• ANGSD may write the major allele as REF;
• the minor allele is written as ALT;
• the assembly reference allele is recorded separately as INFO/RA when available;
• GL, GP and PL values are ordered as major/major, major/minor and minor/minor;
• downstream software should check allele orientation before combining ANGSD output with reference-oriented VCF files.

No allele-ordering or likelihood calculations were changed.

This clarification is related to the allele-polarization question raised in issue #278, but does not change ANGSD’s polarization or SFS calculations.