Question

Haplotypecaller indel realignment

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4.3 years ago

bioguy24 ▴ 230

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 • 1.4k views

ADD COMMENT • link 4.3 years ago by bioguy24 ▴ 230

score 1 · Answer 1 · 2020-01-16

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4.3 years ago

WouterDeCoster 47k

If i am sequencing germline what is recomended?

Follow the GATK best practices.

ADD COMMENT • link 4.3 years ago by WouterDeCoster 47k