Uday Evani
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Recent activity by Uday Evani Sort by recent activity-
Want to report back that workflow successfully completed on the three samples that I was using to test. Is a reference (HG001, HG002) sample always needed when running this workflow? Just want to k...
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I made the changes you suggested and that fixed the original issue and I was able to make considerable progress in running the Joint Genotyping workflow. Currently, I am blocked because I don't hav...
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Unfortunately, more issues. Annotating with TREE_SCORE fixed the runtime issue with ReblockGVCF and the output has the RAW_GT_COUNT but it's missing the TREE_SCORE annotation. The other issue is Ge...
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Yes, we have the TREE_SCORE annotation in our final VCF. I see there is a MoveAnnotationsToGvcf task in your workflow which you are running before ReblockGVCF. So I will do the same and run the mov...
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I looked into this a bit more and found that when I exclude the "tree_score_cutoff" argument the job completes within a minute on the test sample. Can you confirm if you were running with the "tree...
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This is really weird. I am running this step on our on-prem cluster and the files are all local and I haven't noticed any slowness with other jobs. As you can see in the log below, it starts proces...
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Hi Megan, I ran ReblockGVCF as you suggested and that seems to have fixed the missing annotation error that I was getting at the CalculateAverageCombinedAnnotations step but the step takes a long t...
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Yes, I can run the ReblockGVCFs step on the input gVCFs and then run them through Joint Genotyping. Thanks for looking into it. I will get back to you on how that goes.
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Hi Megan, I ran GenotypeGVCFs from version 4.3.0.0 and that failed to annotate as well. I uploaded a tar.gz file to your ftp with a couple of small gVCFs that you can use for testing. Please let me...
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Thank you for pointing to the link describing the difference between AD and DP calculation. That was helpful. I am still a bit unclear especially because this article, https://gatk.broadinstitute.o...