Report the posterior probability of an allele being present in one or more samples. This is the same value as used as in the --haplotype-posterior-threshold option. This should be reported as an info field using the tag APP or similar. It could also optionally be reported per sample?
This can be used as a measure of confidence for each allele being a 'real' allele. In combination with #161, this would allow for an easy mechanism to remove 'noise' alleles from an output VCF (as oposed to adding the --haplotype-posterior-threshold option to MCHap call).
It could also potentially be used as the prior allele frequencies (automatically normalized) when relationships among samples are unknown as it weights against spurious alleles.
timothymillar
commented
1 year ago
Report the posterior probability of an allele being present in one or more samples. This is the same value as used as in the
--haplotype-posterior-thresholdoption. This should be reported as an info field using the tag APP or similar. It could also optionally be reported per sample?This can be used as a measure of confidence for each allele being a 'real' allele. In combination with #161, this would allow for an easy mechanism to remove 'noise' alleles from an output VCF (as oposed to adding the
--haplotype-posterior-thresholdoption to MCHap call).It could also potentially be used as the prior allele frequencies (automatically normalized) when relationships among samples are unknown as it weights against spurious alleles.