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

Using CrosscheckFingerprints for panelseq data


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    Chris Kachulis

    Hi Shashwat Sahay,

    Yes, you can use CrosscheckFIngerprints for panel data.

    The low LOD scores you are seeing generally imply that not very many of the fingerprinting sites are well covered.  This could either be due to very few of the fingerprinting sites being covered by your targets, or your data having low coverage in general.

    You could adjust the LOD_THRESHOLD parameter for you data, but this will increase the chances that the conclusion of the tool will be incorrect.

    A better approach, imo, would be to use a fingerprint map that is better suited to your data (ie, one where more sites are covered).  You could probably spend a bunch of time trying to optimize for your particular data type, but I think a much faster, and nearly as effective approach would be to just grab one of the fingerprinting maps from here and try using that (shouldn't really matter which one, just make sure it's the correct reference).  These maps contain way more sites than the standard maps that are generally used, so you should see your LOD scores increase significantly. 

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