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Hello,
I'm trying to run DeepVariant using ultima data (cram file).
I get information that deepvariant tool provides --enable_joint_realignment and --p_error in DeepVariant 1.5.0 release page.
Bu…
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Hello,
I am having issues running `bcftools +liftover` for some of our samples, which are exome VCF files from single individuals. I am running `bcftools 1.16 / Using htslib 1.16`.
I get the f…
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What to show in the Variant View
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Hello Team,
I am trying to use PureCN with a matched tumor and normal samples, however, it's throwing an error. I am attaching the log file here. I have used CNVkit for segmentation and Mutect2 (G…
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Any hope of getting a university-wide DRAGEN licence?
> The best-performing short-read submissions used statistical variant-calling algorithms with a graph reference rather than a standard linear r…
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Hello,
We are integrating GRIDSS into an analysis pipeline and we would like to retrieve the genomic positions of the supporting reads of specific variants. We currently query the assemblies and th…
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Hi all,
I'm getting an error with intervaltree while uploading the research SV VCF.
My pipeline is essentially to merge together multiple small cohorts of manta SV calls into one larger cohort usi…
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Hello
I am about to call variants in about 200 bam files each about the size of 100GB. I will need 20 TB just to store them in one place. Since currently I do not have this volume, I was thinking t…
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Hi,
First thank you for such a great package.
I have been working on retrieval of gene data of certain variants through gwasrapidd package. I realized that variants can have incompatible gene data…
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**Describe the bug**
A user reports that a batch job comprising just deletion variants taken from ClinVar has failed to complete. The variants are in the attached file `clinvar_hgvs2.txt`.
Several…