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What is the size of the internal window used by gatk haplotypecaller's sliding window approach?

aliceZ2017aliceZ2017 VancouverMember

Hello gatk community,

Since gatk haplotypecaller is ran by a sliding window approach, the variant calling on each position seems to also depend on the presence/type/absence of variants on the flanking region. I guess such effects will stem from the size used by the sliding window. For example, a longer flanking region that contains more variants will tend to help a new read to be better aligned on the current position as I suppose. Could you please let me know what is the internal sliding window size used by gatk HC?

Thank you!


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Hi Alice, technically there are two phases; one involving a sliding window to calculate the activity profile, and the second, some logic to define "active regions" based on the activity profile. Assembly and variant calling are then performed within individual active regions. These processes are described in more detail in the documentation.
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