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gatk-workflows / five-dollar-genome-analysis-pipeline

Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
https://gatk.broadinstitute.org/hc/en-us
BSD 3-Clause "New" or "Revised" License
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PCR INDEL model #28

Open mp15 opened 4 years ago

mp15 commented 4 years ago

Hi,

I notice that this pipeline doesn't specify a PCR indel model, though in your manual for HaplotypeCaller you state in big bold capitals "VERY IMPORTANT: when using PCR-free sequencing data we definitely recommend setting this argument to NONE.". Was this an oversight?