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GenotypeGVCFs

Dear GATK team,
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.html
“GenotypeGVCFs merges gVCF records that were produced as part of the reference model-based variant discovery pipeline (see documentation for more details) using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode of the HaplotypeCaller. This tool performs the multi-sample joint aggregation step and merges the records together in a sophisticated manner. At all positions of the target, this tool will combine all spanning records, produce correct genotype likelihoods, re-genotype the newly merged record, and then re-annotate it. Note that this tool cannot work with just any gVCF files - they must have been produced with the HaplotypeCaller, which uses a sophisticated reference model to produce accurate genotype likelihoods for every position in the target.”

The final sentence says that "accurate genotype likelihoods", how do you define "accurate"? May I ask if it is fully evaluated? If so, could you please tell me how you do the evaluation?

Thank you in advance.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @SiyangLiu‌,

    The genotype likelihoods express the confidence we have in the genotype calls based on the available information. They are accurate in the mathematical sense, given certain assumptions used in the underlying statistical model. Evaluation of the methods is done with several complementary approaches including gold standard datasets and a knowledge base that allows us to empirically verify the quality of the results produced by the program.

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