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Hi,
I am wondering if anyone has ever come across this GATK error during the VariantRecalibrator step
I am wondering if anyone has ever come across this GATK error during the VariantRecalibrator step
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Last edited by medalofhonour; 10-09-2013, 10:26 AM. -
Yes, I've seen it. The error message says "Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself." so I had assumed that it was my mistake, something wrong with the command line. I reran VariantRecalibration with only the minimum of annotations, e.g. -an BaseQRankSum -an FS, and the error went away, so I assume it is when you are trying to use an annotation which only has minimal representation/information in the training variants in the input callset.
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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