Shulou(Shulou.com)06/01 Report--

How to calculate Inbreeding coefficient in GATK, in view of this problem, this article introduces the corresponding analysis and solution in detail, hoping to help more partners who want to solve this problem to find a more simple and feasible method.

As for the definition of inbreeding coefficient, in addition to English materials, there is also a very clear definition in Chinese. Here is a quote:

Inbreeding coefficient (inbreeding coefficient) means that according to the generation generation of inbreeding, the degree of gene purification is expressed as a percentage of inbreeding coefficient, and it also refers to the percentage of homozygous genes or homozygotes when individuals reduce heterogeneous genes as a result of inbreeding, which is generally expressed by F or f.

The program for calculating GATK inbreeding coefficient can be found on github: AS_InbreedingCoeff.java

The code is not short, but the calculation idea is very simple and easy to understand. Here, I mainly show the core of this calculation and make some comments in the code, as follows:

Protected double calculateIC (final VariantContext vc, final Allele altAllele) {

Final int AN = vc.getCalledChrCount ()

Final double altAF

Final double hetCount = heterozygosityUtils.getHetCount (vc, altAllele)

/ / shortcut to get a value closer to the non-alleleSpecific value for bialleleics

Final double F

If (vc.isBiallelic ()) {

Double refAC = heterozygosityUtils.getAlleleCount (vc, vc.getReference ())

Double altAC = heterozygosityUtils.getAlleleCount (vc, altAllele)

Double refAF = refAC/ (altAC+refAC); altAF = 1-refAF

/ / inbreeding coefficient F = 1.0-(hetCount / (2.0 * refAF * altAF * (double) heterozygosityUtils.getSampleCount ()

} 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

/ / calculate inbreeding coefficient

/ / heterozygosityUtils.getSampleCount () get the total number of samples F = 1.0-(hetCount / (2.0 * (1-altAF) * altAF * (double) heterozygosityUtils.getSampleCount ();}

Return F;}

Calculated by using Hardy Weinberg's law: 1. 0-(hetCount / (2-altAF) altAF (double) N, where N is the number of people. This value gives the number of expected heterozygous variants. So the parameter F (inbreeding coefficient) is the difference between "actual hetCount" divided by "expected hetCount" and 1.0. When the F value is closer to 0, it means that the actual hetCount is closer to the theoretical hetCount.

This is the answer to the question about how to calculate Inbreeding coefficient in GATK. I hope the above content can be of some help to you. If you still have a lot of doubts to solve, you can follow the industry information channel for more related knowledge.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.