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This is not exactly new (it was fixed in GATK 3.0) but it's come to our attention that many people are unaware of this bug, so we want to spread the word since it might have some important impacts on people's results.
Affected versions: 2.x versions up to 2.8 (not sure when it started)
Affected tool: SelectVariants
Trigger conditions: Extracting a subset of samples with SelectVariants while using multi-threading (
Effects: Genotype-level fields (such as AD) swapped among samples
This bug no longer affects any tools in versions 3.0 and above, but callsets generated with earlier versions may need to be checked for consistency of genotype-level annotations. Our sincere apologies if you have been affected by this bug, and our thanks to the users who reported experiencing this issue.
Geraldine Van der Auwera, PhD