Ury Alon
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Activity overview
Latest activity by Ury Alon-
Ury Alon commented,
Hi, I'm using MarkDuplicatesSpark to merge large lane BAM files. The command fails with the following output: ...WARN HtsjdkReadsRddStorage: Unrecognized write option: DISABLEUsing GATK jar /opt/bi...
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Ury Alon commented,
Awesome, thank you very much Geraldine Van der Auwera. I'll get to it :)
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Ury Alon commented,
Great, thanks for clarifying. In our case, processing time is usually prioritized over costs, but we try to have both :) What I meant is, should there be a difference (in terms of identifying muta...
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Ury Alon commented,
Thanks Geraldine Van der Auwera, I've been actually reading this link earlier today :) I don't know if this is the place to get more specific, but I'll give it a try: In terms of optimizations, we'...
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Ury Alon commented,
Thanks for the prompt response, Geraldine Van der Auwera. We are not using actual WDLs, as we use AWS Step Functions and Batch for pipeline orchestration and execution. We have done significant op...
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Ury Alon commented,
Hi Geraldine Van der Auwera, Now that v4.2.0.0 is released, are there any news regarding the DRAGEN-GATK somatic short variants pipeline (Mutect2) implementations? I am using the software-only ver...
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Ury Alon commented,
@Amin, thanks for verifying this.
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Ury Alon commented,
Thanks for the great explanation. Regarding the following line: "Note that we used to do a first round of marking duplicates here for QC purposes but tool improvements have rendered this obsolete" ...
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Ury Alon commented,
I ended up taking "real" 4-lane FASTQ files (huge ones), truncating them and hoping for the best. It turns out the problem before was in the data, as I suspected, and this time I succeeded to go fr...
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Ury Alon commented,
Hi @danilovkiri, Thanks for finding the cause for this error. I've been taking my time setting up a fully reproducible environment for running the discussed pipeline over test data, based on the su...