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We're trying to use SNParcher on some fairly large genomic datasets at the moment (2000 + individuals), and I am anticipating a lot of slow-down at genotyping steps. I was wondering if it's possible t…
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Hi @lh3,
I'm building an assembly-based small variant truth set for NA12878, leveraging assemblies from across the CEPH pedigree and validating inheritance patterns in eight third-generation family…
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There is already an old branch, that should be doing most of it. But it needs to be retested. https://github.com/akoch-yatta/eclipse.platform.swt/tree/use-dpi-dependent-win32-api-calls
One old issue …
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**Expected Behavior**
For FormLoginConfigurer, builder chain defaultSuccessUrl()..successHandler() applies results from both methods
**Current Behavior**
Because defaultSuccessUrl() creates its…
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**Is your feature request related to a problem? Please describe.**
Some variant calls might be incorrect or need to be adjusted to take multinucleotide variants into account. Currently the user might…
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So I noticed that in the main vg git repo README that they recommend normalizing the variant calls for comparison purposes. https://github.com/vgteam/vg#variant-calling
Should this be incorporated …
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Greetings,
Thank you so much for this amazing tool!
So I am checking the consistency between the SV calls after randomizing and splitting the reads into two equal datasets. Each dataset is of arou…
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Hi,
I am currently attempting to perform an association analysis on noncoding regions using WES data. However, while executing 379 array jobs, some of the jobs failed with an error. Could this iss…
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We are performing somatic variant calling in tumour-only mode where we call variants with both Mutect2 (GATK version 4.1.2.0) and Vardict-java. We have noticed that Mutect2 calls adjacent phased indel…