GATK中如何计算Inbreeding coefficient（近交系数）

protected double calculateIC(final VariantContext vc, final Allele altAllele) {
    final int AN = vc.getCalledChrCount();
    final double altAF;
    final double hetCount = heterozygosityUtils.getHetCount(vc, altAllele);
    final double F;
    //shortcut to get a value closer to the non-alleleSpecific value for bialleleics
    if (vc.isBiallelic()) {
        double refAC = heterozygosityUtils.getAlleleCount(vc, vc.getReference());
        double altAC = heterozygosityUtils.getAlleleCount(vc, altAllele);
        double refAF = refAC/(altAC+refAC);
        altAF = 1 - refAF;
        F = 1.0 - (hetCount / (2.0 * refAF * altAF * (double) heterozygosityUtils.getSampleCount())); // inbreeding coefficient
    } else {
        //compare number of hets for this allele (and any other second allele) with the expectation based on AFs
        //derive the altAF from the likelihoods to account for any accumulation of fractional counts from non-primary likelihoods,
        //e.g. for a GQ10 variant, the probability of the call will be ~0.9 and the second best call will be ~0.1 so adding up those 0.1s for het counts can dramatically change the AF compared with integer counts
        altAF = heterozygosityUtils.getAlleleCount(vc, altAllele)/ (double) AN;
        // 计算inbreeding coefficient
        F = 1.0 - (hetCount / (2.0 * (1 - altAF) * altAF * (double) heterozygosityUtils.getSampleCount())); // heterozygosityUtils.getSampleCount() 获取总样本数 
    }
    return F;
}