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

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    Charlie Murphy

    I am really interested in possibly using this tool in my pipeline. However, I have some questions about some of the output metrics that I cannot find information about in this documentation. Specifically, how do "LOD_SCORE", "LOD_SCORE_TUMOR_NORMAL", and "LOD_SCORE_NORMAL_TUMOR" differ exactly? I know the latter two are somehow less sensitive to loss of heterozygosity, but I wonder if you could be more specific? Do they just restrict their analysis to homozygous sites or something?

    Thanks!

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