Haplotypecaller indel realignment

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

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written 6.6 years ago by bioguy24

1 answer

If i am sequencing germline what is recomended?

Follow the GATK best practices.

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written 6.6 years ago by WouterDeCoster

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