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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

Interpretting CrosscheckFingerprints metrics

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    Alijah O'Connor

    There are no descriptions for the fields at http://broadinstitute.github.io/picard/picard-metric-definitions.html#CrosscheckMetric either

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    Bhanu Gandham

    Hi Alijah O'Connor

     

    Thank you for the feedback and we do plan on fixing the descriptions for the fields at http://broadinstitute.github.io/picard/picard-metric-definitions.html#CrosscheckMetric

     

    With regards to your first question: Given that the --INPUT combined_merged_preprocessed.bam includes a single file, CrosscheckFingerprints will crosscheck all samples inside the BAM. Since you have two sample bams in your input (named normal and tumor ), each line in the output LEFT_ and RIGHT_ will identify which samples are being crosschecked. The LOD score will inform the probability that samples match and tumor-aware LOD score will help access identity in presence of severe loss of heterozygosity.

    Each comparison is between a "left" group of inputs and a "right" group. For example, a group could be 1) a read-group, or 2) all the readgroups that belong to a certain sample, or 3) everything from a certain file. This grouping is controlled by the CROSSCHECK_BY argument. Once you know what the groups are, the group value is simply something that identifies that group....for example, 1) a readgroup by its PU field, 2) a sample is identified by the sample ID and 3) the file by its path.
     
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    Alijah O'Connor

    Thanks for clarifying some of this Bhanu Gandham, though I would like to mention that compared to many of the other GATK tools, I find the documentation of this tool to be quite confusing. I'm not sure how many users use this tool, but I think it would be helpful to those that do use it to either write a forum article for this one or buffing the documentation, perhaps with a few examples.

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