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

GenomeStrip prepare summary metadata by chromosome?



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    Here attached the reply from Bob, hope can help you.


    Certainly we do #2 all the time, so that is definitely a well-known path. As to #1, I have not personally tried or benchmarked it. I do know that if you take the genome-wide quantities from preprocessing for one chromosome and compare them to a different chromosome or the whole genome, there can be deviations that will change the results.

    The main thing I would worry about are aneuploidies or perhaps large mosaic gains/losses that affect a large segment of a chromosome. This will distort the read depth estimation for that chromosome. If there is a large aneuploidy, this will also have small effect if you do #2, but because an aneuploidy on one chromosome is averaged with all of the others, the effect is usually small enough to not make much difference.

    Hope this helps,


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    Bhanu Gandham

    Hi Bob Handsaker


    Could you please take a look at this question. thank you!

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