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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

Picard CrosscheckFingerprints not identifying samples from the same individual as a MATCH


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    Genevieve Brandt (she/her)

    Hi Christopher Sisk,

    Thanks for writing in about this question! Hopefully we can help to figure out why you are seeing this.

    First, something to know, is that contaminated samples can erroneously be labeled as mismatching, so there might be contamination in one of your samples. We recommend trying verifyBAMid to check. If there is contamination, you might be able to extract a cleaner fingerprint with ExtractFingerprint. If both samples are contaminated, this might not work as well, though, because the local relative coverage could differ between the two original (uncontaminated) samples.

    You can try to manually examine the SNPs to determine which are causing the negative LOD score. One way to do that is to run ExtractFingerprint on one of the samples to get a VCF then CheckFingerprint, which gives a metrics file.

    You can also examine the samples in IGV and walk through the fingerprinting sites. You can then see where the genotypes are the same in both samples and different. 

    Let me know if you have any further questions and if this ends up working for you.



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