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?


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    Yunjiao Zhu

    Saving some searches for anyone having the same question:

    By Genevieve Brandt (she/her) from the GATK team:

    "I was able to find out more information about the LOD_SCORE_TUMOR_NORMAL vs the normal LOD_SCORE. The normal LOD_SCORE is the log odds ratio that the identity of the two samples is the same, if they are typical samples. If the two samples that are being compared have the same identity, but one is a tumor sample and one is a normal sample, you can use the LOD_SCORE_TUMOR_NORMAL or the LOD_SCORE_NORMAL_TUMOR. Tumor samples can have a loss of heterozygosity which can make them appear as if they are an "impure" version of the sample. The LOD_SCORE_TUMOR_NORMAL is the log odds ratio that the samples have the same identity, but the first sample is a tumor sample and the second is a normal sample. The LOD_SCORE_NORMAL_TUMOR is the opposite, if the first sample is a normal and the second is a tumor sample. "

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