Haplotypecaller indel realignment
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21 months ago
bioguy24 ▴ 220

Is there a way to disable indel realignment in haplotypecaller or is that determained bu the -minPruning? If i am sequencing germline what is recomended? Thanks :)

haplotypecaller • 769 views
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Entering edit mode
21 months ago

If i am sequencing germline what is recomended?

Follow the GATK best practices.

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