Uday Evani
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Activity overview
Latest activity by Uday Evani-
Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani commented,
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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Uday Evani created a post,
Missing RawGtCount annoation from GenotypeGVCF output
The GenotypeGVCF task in the UltimaGenomicsJointGenotyping.wdl completes successfully but does not add the RawGtCount annotation to the VCF because of which the next step, CalculateAverageAnnotatio...