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All tools in 'NGS: Indel Analysis' are missing on GVL-3.05:
NGS: Indel Analysis
- Filter Indels for SAM
- Indel Analysis Table for combining indel interval data
- Indel Analysis
One tool (Indel Anal…
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I run seGMM using command:seGMM -vcf /ddn/data/BDC/Analysis/NGS_Analysis/habusamra/230920_A00840_0041_AHGMT3DRX3/Alignment_Germline_Aziz/PBG-862-23_S3_HaplotypeCaller.vcf -i test.txt -a BAM -t WES -n…
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I'm am struggling to install presto and no one else seems to be having the same issue. Here is the error message I get:
```
> devtools::install_github("immunogenomics/presto")
Downloading GitHub …
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Hi,
Thanks very much for the great tool. We've been trying CRAQ out in several of our assembly projects and we sometimes run into strange behavior where analysis seems to finish ok, but low_confidenc…
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Should be a simple fix to ensure that the reference fasta file does not contain empty lines.
I'll likely fork the project soon anyways and will be happy to push the fix.
Trying to get a feel for the …
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Dear Thierry et al.,
I am getting this error when I run assignR:
`Calibrating REF/ALT alleles...
Error in if (detect.gt == "GT_VCF_NUC") { : argument is of length zero`
when I try to run assi…
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Hello,
I am trying to incorporate the ensemble approach in my bcbio analysis and getting errors at the bcbio.variation command for validation of calls. Here are some details,
Run log -
/gpfs/ngs/on…
ssaif updated
9 years ago
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Hello,
I’m trying tor run the analysis on GeoMx data following the guide here: https://bioconductor.org/packages/3.14/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#
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Hi facing a issue in grouping step. Any suggestion?
Running grouping. Command line:
java -jar /data/HG135/DEL_AnalysisToolkit_NAR_20230215.jar grouping -ctrl S5 -G S1:S3:S5 -S /data/HG135/rcd135_2…