Anton Kovalsky
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Activity overview
Latest activity by Anton Kovalsky-
Anton Kovalsky commented,
Hi @anna The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a ba...
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Anton Kovalsky commented,
Hi wannamd The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a ...
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Anton Kovalsky created an article,
Mutect2 Webinar Announcement and A Call for Questions From Our Community
Do you miss the in-person GATK workshops we used to host back in pre-pandemic times, and the interactions that came about as a result? So do we! Hosting lively discussions has always been an import...
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Anton Kovalsky commented,
Official comment Hi Vincent Hahaut thanks for your question.It looks like you may be missing the barcode in LIBRARYPARAM_SAMPLESHEET.The LIBRARYPARAM_SAMPLESHEET needs to have the barcodes associated with the reads...
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Anton Kovalsky commented,
Hi Jose Luis Gualdron thanks for your post.The --genomicsdb-update-workspace-path option was added well after 4.0.12.0, which is why you see an error with that version. In the second step, If the G...
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Anton Kovalsky commented,
Hi JonR thanks for your post! It looks like this has been a recently documented issue that should be resolved in the near future. You can find more information about this issue here:https://github....
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Anton Kovalsky commented,
Hi Surdan Burasi, genomicsdbimport merges the single gvcfs into a cohort gvcf and then genotypegvcfs converts that to a vcf.
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Anton Kovalsky commented,
Hi paruchuri anoosha, thanks for your question, could you please provide IGV screenshots where you observe the expected variant sorted by base, the allele counts reported by IGV, and a description ...
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Anton Kovalsky commented,
For now, a workaround might be to pull out those variants. We haven't fully characterized what's causing this, so we can't easily predict which variants will cause the problem, so you would need to...
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Anton Kovalsky commented,
Hi lck, thanks for you post, this is indeed a known issue. You can follow our updates on fixes related to the StringIndexOutOfBoundsException error here and here