James Emery
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Activity overview
Latest activity by James Emery-
James Emery commented,
Hello Katherine Fawcett. If you want the GATK to output a GVCF you use the extra flag `--ERC GVCF` which makes the HaplotypeCaller produce a GVCF instead of a VCF. This is compatible with `--dragen...
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James Emery commented,
Hello Mickaël Mendez. SplitNCigar reads has a few extra steps that you might not know about that can result in the sort of behavior you are seeing here. Specifically SplitNCigar reads is internally...
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James Emery commented,
Hi Marc Crepeau. I have looked at your example and there is indeed a problem with our code related to the --alleles mode. Specifically very long deletions can cause indexing issues when they get in...
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James Emery commented,
Hello Marc Crepeau. It is useful context to hear that you are enocuntering a similar failure with --alleles set. It would help us immensely to track down the issue to have some test data to debug w...
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James Emery commented,
Hello Wannes Dermauw. We do have an argument that does very closely match with what you are asking for. There are a number of calling thresholds/heuristics that can cause variants to be assembled b...
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James Emery commented,
Hello Geert Vandeweyer. Likely this is an inherent issue with the size of the assembly window and very long indel events that in Alleles mode that we should fix. However for us to be sure about tha...
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James Emery commented,
Hello Rolf Schröder. I'm sorry to hear about this issue with HaplotypeCaller. It seems like you have already found exactly the link with advice that we usually deploy in these situations. Looking a...
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James Emery commented,
Hello UTao Cao. This error looks like a genuine bug that we probably have to fix. It would help us to run this to ground if you can test a few things for us. First can you try running PrintReads on...
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James Emery commented,
Hello mengting. The error message in question here implies that you are trying to overwrite an existing directory. First I would recommend making sure that wherever you are writing your outputs tha...
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James Emery commented,
We have some generic advice for finding missing variants in the HC here: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-vari...