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Questions about Genotype Refinement

Hi, I am newer to this filed and your help is very much appreciated:

I followed the core GATK Best Practices workflow, and now comes to the Genotype Refinement workflow. I have some questions about this:

  1. For the tool CalculateGenotypePosteriors, there is a note that By default, priors will be applied to each variant separately, provided each variant features data from at least 10 called samples (no-calls do not count). I have only 8 samples in my cohort vcf file. Does it make sense to do the refinement step on this small dataset?

  2. For the tool VariantAnnotator, there is an option -I input.bam. Is the input.bam the one generated by BQSR? In my case, I have 8 bam files, and should I provide all these bam files with multiple -I option?

Sorry for my naive questions.

Best wishes

Answers

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