shanzor ✭
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- shanzor
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- canberra
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Thanks the update seems to have fixed it. Thanks!
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I should have noted, the filter expressions I used are as follows: --genotypeFilterExpression "DP < 10" --genotypeFilterName low_cov --genotypeFilterExpression "GQ < 30" --genotypeFilterName low_GQ
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My bad, I hadn't reset the environment. Working now with --setFilteredGtToNocall. Thanks!
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Tried using 3.4.46. I think this is the latest version? Still getting the same Error. Actually there are two versions of this argument presented on the gatk web documentation at present. --setFilteredGtToNocall and --setFilteredGenotypes…
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Thanks I'll update and try again.