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Input Priors HaplotypeCaller and GenotypeGVCFs

Hi,

Both HaplotypeCaller and GenotypeGVCFs have --input_prior options.

I'm confused on whether both need to be changed or just in Haplotypecaller to remove reference bias. Previous posts mention changing the --input_prior in HaplotypeCaller but not GenotypeGCVFs

(https://gatkforums.broadinstitute.org/gatk/discussion/11877/free-of-reference-bias-priors-in-haplotypecaller)

Also, say if I created gVCFs and forgot to change the --input_prior, can i just change the priors at the GenotypeGCVFs step instead of creating the gVCFs again with the correct priors.

Thanks,
Mo

Answers

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