Improve handeling of allele priors and reference allele - Githubissues

PlantandFoodResearch / MCHap

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

MIT License

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Improve handeling of allele priors and reference allele #147

Closed timothymillar closed 2 years ago

timothymillar commented 2 years ago

New Features:

Mask reference allele when it is only reported to satisfy VCF spec #146
Optionally report prior allele frequencies in AFPRIOR field
Filtering for some edge cases where genotypes should not be reported (AF0 and NOA)

Bug Fixes:

Handle edge-case where all prior allele frequencies are zero #145

VCF Changes:

Added REFMASKED info flag to indicate reference allele is amsked and should be ignored
Added AFPRIOR infor filed to indicate prior allele frequencies
Added NOA filter to indicate loci where no alleles were observed (e.g., masked reference only)
Added AF0 filter to indicate invalid prior allele frequencies in which all frequencies were zero