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Hi there,
I am using maftools in RStudio. With the included/example laml maf file I am able to plot an oncoplot and sort by a clinical feature. It works beautifully. Below is the plot I get when I …
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Hello,
The latest version of ANNOVAR (2018Apr16) in my computer, however web-based checking to see whether ANNOVAR new version is available ... Failed
Database also cannot be downloaded.
How to s…
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I'm trying to apply filters using --info field for my ANNOVAR annotated VCF.
I'm able to run this expression for **gnomAD_genome_ALL** filtering:
```
~/resources/slivar expr \
--pass-only \
--…
nroak updated
5 years ago
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The script `familyKeyMatchingAfterANNOVAR.py` should take a multi sample "GenomeAnnotationsCombined" ANNOVAR file as input and match shared homozygous or heterozygous genotypes for selected samples an…
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Annovar in annovarForMpa module should be given the possibility to be mutlithreaded using option -thread nb_thread, variable passed via the inputs.json file
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In conjunction with #9 need to consider alternative staging methods for reference files, especially in cases where a path to an entire directory is passed such as for ANNOVAR databases and some genome…
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Hi,
I'm trying the following command
**perl annotate_variation.pl -downdb -webfrom annovar --buildver hg19 1000g2015aug humandb/**
**perl annotate_variation.pl -downdb -webfrom annovar --buildve…
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Hi,
I am trying to annotate some samples and when reading the gene_fullxref.txt file the software crashes. I read the error but I do not understand it at all. Could you give me a clue?
This was my…
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The Polyphen scoring seem to be missing in both hg19/hg38. For example:
wget http://www.openbioinformatics.org/annovar/download/hg19_dbnsfp35c.txt.gz
gunzip hg19_dbnsfp35c.txt.gz
grep…
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Exceptionally I receive the error below when parsing output from snpEff (not all my vcf files return the error)
I assume some discrepency between the FORMAT info fields and the content of the vcf lin…