Should it say "AC>0" in the --input_prior documentation for the HaplotypeCaller?

saeschbasaeschba SwitzerlandMember

In the documentation of the --input_prior argument of the HaplotypeCaller (https://software.broadinstitute.org/gatk/gatkdocs/current/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php#--input_prior) it says that the argument allows to "specify a list of probabilities for each AC>1 to be used as priors for genotyping". However, should that not say "...for each AC>0 to be used..." instead? The example that is shown in the documentation is for a single-sample diploid case, i.e. for N = 1. Obviously, AC can take the values 0, 1, and 2. In the example, two -inputPrior arguments are provided, in line with the rule that 2*N arguments should be provided. The fact that 2 values per sample must be provided suggests that two genotype prior likelihoods must be given. The third is then optained as 1 minus the other two in the diploid case. Hence the conclusion that it should say AC>0 instead of AC>1.

Issue · Github
by Sheila

Issue Number
2021
State
closed
Last Updated
Milestone
Array
Closed By
chandrans

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