Understanding bandPassSigma value in GATK HaplotypeCaller command
0
0
Entering edit mode
14 months ago
Augusta ▴ 20

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 • 297 views
ADD COMMENT

Login before adding your answer.

Traffic: 851 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6