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CommentsRecent activity by Anton Kovalsky Sort by recent activity
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...
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 ...
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...
Hi Jose Luis Gualdron thanks for your post.The --genomicsdb-update-workspace-path option was added well after 18.104.22.168, which is why you see an error with that version. In the second step, If the G...
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....
Hi Surdan Burasi, genomicsdbimport merges the single gvcfs into a cohort gvcf and then genotypegvcfs converts that to a vcf.
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 ...
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...
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
Hi Tamar Lahav, thanks for your question!The BAI file is the index for the BAM that allows for querying different positions, so both are necessary when you want to subset your data. GATK tools that...