Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

LearnReadOrientationModel Follow

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    David Lord

    I'm currentlly conducting somatic variant calling through Mutect2 and I plan to use the LearnReadOrientationModel tool (my data is derived from FFPE tumor samples). Should I create the orientation model (LearnReadOrientationModel) using multiple f1r2 inputs and then pass this singular model to FilterMutectCalls? Or should I rather generate one model for each normal-tumor pair and then pass each corresponding model to the filtering of each VCF? :) 

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