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I having trouble removing multi-allelic annotations from the dbNSFP reference text file, as it seems to always parse these fields as 'self'. I am thinking the problem has to do with limitations in par…
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Specifically, the `data_dir` field stores a full path to the file, rather than relative to MEDIA ROOT. In most cases we won't be moving the filesystem around so it's not urgent to fix this.
To fix th…
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The tool failed with error missing Java
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I have already been using Adam with snpEff annotations and it worked great. However, when I've tried to use it with a VCF file annotated using Ensembl VEP it didn't work. I was expecting, that ANN for…
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Thank you for the useful script, but I noticed an error in my output for kaks.py. Because the script totals the numbers of missense and sense SNPs per gene, I found the counts to be redundant for gene…
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python /home/kpadmin/biosoft/TMB/bin/pyTMB.py -i /home/kpadmin/TMB/LST_norm.vcf --effGenomeSize 33280000 --dbConfig /home/kpadmin/biosoft/TMB/config/snpeff.yml --varConfig /home/kpadmin/biosoft/TMB/co…
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Installed snippy in conda environment in ubuntu 20.04 LTS. Following message was obtained. Assistance will be greatly appreciated.
![Capture](https://user-images.githubusercontent.com/89452811/130594…
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## Compile list of Modules to add for Docker Build
module=['vcf2maf/1.6.21','VEP/102']
module=['fastq_screen/0.15.2','bowtie/2-2.5.1']
module=['kraken/2.1.2', 'kronatools/2.8']
mod…
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Hi,
After we called variants using the GATK pipeline, is there a way to annotate the variants as synonymous or non-synonymous using ORF annotations generated by Transdecoder?
Thank you so much!
Shu
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We could choose together which columns are displayed by default.