Understanding bandPassSigma value in GATK HaplotypeCaller command
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4.3 years ago
Augusta ▴ 30

Hello everybody,

I am working on the interpretation of VCF files called with HaplotypeCaller 3.

In the file headers, I can see that bandPassSigma was set to "null". I am unsure as to how interpret this vaIue. Does it mean that the default (17bp, according to the tool documentation) was used? I am confused about this because all other default values are written out (e.g. activeProbabilityThreshold=0.002).

Any help will be very much appeciated!

GATK HaplotypeCaller bandPassSigma Variant Calling • 698 views
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