Graeme Thorn
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Latest activity by Graeme Thorn-
Graeme Thorn commented,
Hi Genevieve, That seems to have fixed it - I've also pre-emptively changed the other filter names to remove the spaces. It obviously is how GATK4 deals with the strings in the filter names compare...
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Graeme Thorn commented,
Hi Genevieve, I have tried changing the filter expression to "DP < 10.0", but still get the same error. One thing I did find with switching from GATK3(.8) to GATK4 was that I needed to index the fi...
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Graeme Thorn created a post,
Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character
AnsweredI'm having an issue with VariantFiltration on GATK v4.1.2: one of my filters is claimed to not satisfy the regex required, but I have examined the command line and found no issues with it. Details:...
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Graeme Thorn created a post,
Hard filters on VariantFiltration following HaplotypeCaller; multiple warnings
I'm applying some hard filters at the end of a pipeline where the previous step is HaplotypeCaller. However, in the error log of VariantFiltration there are multiple lines of the following: WARN 1...