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How does HaplotypeCaller identify potentially variable regions?

aciolfiaciolfi Posts: 6Member
edited July 2013 in Ask the GATK team

Hi there,

I'm starting to use use the HaplotypeCaller to identify variants in my exome projects, but I was wondering how it initially determines if a region has the potential to be variable. I couldn't find any useful documentation, could anyone of you help me to basically understand this first step?

Thank you in advance.

Post edited by aciolfi on

Best Answer


  • aciolfiaciolfi Posts: 6Member

    Thank you Geraldine: yes, I was asking about the general principle behind the HC selection of the active regions.

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