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

Does the CN with LQ need to be deleted?



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    Genevieve Brandt (she/her)

    Thank you for your post. Bob Handsaker has been tagged and will get back to you shortly.

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    Bob Handsaker

    I'm assuming you mean genotypes with "LQ" as the value of the FT tag in the genotype field. The LQ filter value is simply a shorthand for CNQ < 13 (or roughly 95% confidence) in the diploid copy number estimate. Whether you want to use these genotypes or not depends on what you want to do.

    For the coefficient of variation (of the true copy number), my reaction without thinking about it too hard is that dropping all LQ genotypes would probably lead to a biased estimate since DNA samples with higher copy number will tend to have less confident genotypes, which will bias downward the estimate of both the standard deviation and the mean. I.e. it is harder to tell CN 9 from CN 8 than it is to tell CN 2 from CN 3 or CN 1.

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