Category: annovar

Variants in untargeted genes identified after atrgeted exome sequencing analysis

Variants in untargeted genes identified after atrgeted exome sequencing analysis 0 Hi, I recently analyzed some targeted exome sequencing samples, which were provided to us by our collaborators, for which I do not possess the target gene list. Upon analysis, I am informed that some of the genes – whose…

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Annovar on galaxy v 0.2 is not working

Annovar on galaxy v 0.2 is not working 0 Hello, I have to finish a project for an online course where I need to identify DNA polymorphic sites through galaxy. I want to annotate vcf file generated after free Bayes step. I am new to this analysis part and I…

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Unable to overcome troubles in whole exome analysis

Unable to overcome troubles in whole exome analysis 0 Hi, I am working on whole exome sequencing data whose pipeline has been standardized in the lab as such – Align with bwa-mem –> SortSam based on coordinates with Picard –> MarkDuplicates –> Remove sequencing duplicates –> Variant calling –> BQSR…

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How to get vaf information column using annovartomaf

How to get vaf information column using annovartomaf 0 Hi, I am trying inferHeterogeneity function in R. I converted my annovar output to maf file using annovartomaf according to the toolsheet. But I can not get t_vaf containing vaf information. I also don’t have i_TumorVAF_WU. My annovar output file has…

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How to get vafCol converting annovar outputs to maf object

How to get vafCol converting annovar outputs to maf object 0 Hi, I am trying to find heterogeneity in tumor samples using maftools. I have annovar outputs and converted them to maf object using annovarToMaf function. var.annovar = system.file(“extdata”, “variants.hg19_multianno.txt”, package = “maftools”) var.annovar.maf = annovarToMaf(annovar = var.annovar, Center=”CSI-NUS”, refBuild…

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converting annovar format file to maf by annovarToMaf

converting annovar format file to maf by annovarToMaf 0 Hi, I have annovar format file and want to convert it to maf , and to this aim, I use the annovarToMaf: library(maftools) var.annovar <- system.file(“extdata”, “ann_test.txt”, package = “maftools”) var.annovar.maf <- annovarToMaf(annovar = “ann_test.txt”, Center=”CSI-NUS”, refBuild = ‘hg19’, table=”refGene”, MAFobj…

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Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation

Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation 1 I would like to analyze the functional consequence of the mutation in the protein-coding region of the human genome like in TP53 or EGFR etc. I tried Annovar, VEP, SIFT, polyphen, etc but as far…

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Annovar: Mouse database download

Annovar: Mouse database download 1 Hi there, I want to work with specific mouse strain from ucsc browser (A/J) on my annovar. How do I download it? perl annotate_variation.pl -buildver mm10 -downdb -webfrom annovar refGene mousedb –> is for mm10 db I have tried –> perl annotate_variation.pl -buildver 16 Strains…

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Assistant Research Professor – Genomics and Bioinformatics job with City of Hope

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…

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Variant filtration software

There are tools like ANNOVAR, SnpEff, and VEP that are widely used for variant annotation. Most variant filtration/prioritization software work on the output from these three main software. Appended below is a list of software that one can use to do variant annotation, filtration, and even prioritization. NOTE: However you…

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