Laura Gauthier
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Recent activity by Laura Gauthier Sort by recent activity-
We only run over the canonical autosomes and allosomes: chr 1-22 plus X and Y. It's not unlikely that the reason the contig ploidy model isn't working is that it can't fit some of the alternate an...
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I don't think this is a python problem, I think this is a data problem. What's in your ploidy priors file? That doesn't look like the one we distribute.
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Hi Jean Paul Ouedraogo, Unfortunately GATK no longer has a dedicated support team, so the developers are pitching in to try and answer as many questions as we can. That said, we don't have time to...
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Hi Sheryl, MarkDuplicates specifically may not use the read group information, but BQSR definitely does. We recommend creating a different FASTQ file for each read group and then converting those ...
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Hi Joanna Griffiths I've worked with GenomicsDB a lot, but I've never seen this error message before. I have one suggestion you can try before we pass this issue on to the GenomicsDB development t...
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Great! And do look into ReblockGVCF like kvn95ss suggested. If you're not super concerned about hom-ref GQ precision, it can be a 90% reduction in GVCF size, which speeds up execution time when t...
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The GermlineCNVCaller and other tools in the gCNV pipeline have the same command syntax as other GATK tools that are exclusively Java. Internally, the tool is referencing the gcnvkernel python pac...
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Hi Sophia I think the most reproducible way to do this would be with Picard IntervalListTools, which you can run from GATK. The interval you're trying to retain will probably have to be in *.inter...
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Y R you might find the corresponding WDL workflow helpful: https://github.com/broadinstitute/gatk/blob/master/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl The diagram is just an overv...
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Hi Matt Johnson The provided WGS calling intervals split at Ns in the reference so there are no boundary effects. However in hg38 there are fewer and fewer of those. In our production pipeline, w...