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Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x), :
duplicate row.names: rs147304884, rs774418471, rs72106118
Calls: runAbsoluteCN ... eval -> as.data.frame -> as.data.fram…
lima1 updated
4 years ago
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There are insignificant differences between InbreedingCoeff when calculated in GATK3 and GATK4. I've tried to recreate these differences and haven't been able to find them when I run with -L over a si…
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Brad,
The other day I was looking at WES data of different read length and evaluated the performance of GATK4 and freebayes using NA12878. When doing a series of analyses with data trimmed to diffe…
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Gatk performance work, do we have output files included in our data bucket? We need to add those so people can compare.
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## Bug Report
### Affected tool(s)
GenotypeGVCFs
### Affected version(s)
4.0.2.0
### Description
After running GenomicsDBImport which takes a short time, GenotypeGVCFs takes a really long time to…
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Dear Team,
Is it possible to pass custom parameter values for the mutect2 variant caller? I would like to pass custom values for the following parameters.
`--normal-lod and --minimum-allele-fr…
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Posting issue on @cmnbroad's request.
I see this stacktrace of a WARN for some GATK tools. The tools proceed to run successfully. For example, LearnReadOrientationModel gives this. I've been prepa…
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I am available to help in this process @jonn-smith. Just to give you an idea of the evolution of tutorials, here are some example tutorials that focus on somatic CNV calling.
- Alpha tutorial that …
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For @droazen on his request. Thank you for looking into this.
[shlee_ref200.zip](https://github.com/broadinstitute/gatk/files/1609980/shlee_ref200.zip)
Observations and commands are in file **s…
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This is kind of different from the previous discussions because it specifically mentions targeted panels. Lots of methods already present in bcbio require at least exome-level coverage (TitanCNA for s…