Get variant type from genotype data

Hi,

I have some mutation data (ex. GSE11417). Is there any way to get the variant types like nonsense, missense, and so on?

type missense mutation nonsense variant

• 1,099 views • link

updated 3.8 years ago by Sam

• written 3.8 years ago by Nemo •

1 answer

Easiest way will be to use the VEP https://useast.ensembl.org/info/docs/tools/vep/index.html

• 0 views • link

written 3.8 years ago by Sam

More posts like this

Question regarding pathways and cell types
written 3.7 years ago by Nemo •

Hi everybody, I have a question regarding the cell types and pathways. First, I would like to get some information about the similarities and differences …
How can I get the number of reads per variant in hisat2?
written 4.0 years ago by Nemo •

Hello, I would like to see how many reads I have per variant. Is there any way to get this information using hisat2 or gatk …
what does non synonymous mutation means?
written 6.6 years ago by huynguyen96.dnu •

I am currently a IT student and try to become a bioinformatician, and that is, I have a little knowledge of molecular biology. Now, perhaps …
Parsing through VCF annotated by Funcotator
written 7.1 years ago by abbysue •

I have a variant set annotated by GATK's Funcotator... creates an extra field in the VCF called "Funcotator" with several [annotations][1] separated by pipe characters. …
Representative AA change from point mutation given by genomic lcus
written 11.4 years ago by sak042 •

We are having a hard time to determine a "representative" amino acid change that resulted from a genomic point mutation. Obviously, a genomic point mutation …
minimum information content in .maf to run mutsig
written 11.8 years ago by shpak.max •

I have been filtering and annotating vcf's generated by SomaticSniper and MuTect, and would like to run my mutation calls through MutSig to identify which …
Using Music When Silent Mutation Is Excluded In Data
written 12.0 years ago by wangjiaqian •

Hello, I have a problem when using Music. Only missense, nonsense, splicing mutations and indels are included in my data, there are no synonymous mutations, …
Using Mutsigcv When Mutation Data Is Not Sufficient
written 12.4 years ago by liyfpaper •

Dear all: I have a problem when using MutsigCV. I sequenced 20 paired tumor and normal tissues, and called somatic mutations including missense, nonsense, splicing …
Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
written 13.4 years ago by Raony Guimarães

Hello All, I'm using annovar (which sometimes uses dbNSFP) for annotating variants against different databases, such as: SIFT, Polyphen2, Mutation Taster and etc Let's say …
How To Check If The Iupac Snp Code Changes Translation ?
written 16.0 years ago by jvijai

So, I have data from an exome sequencing. I also have the SNP calls from Bioscope. My question is how to check if the IUPAC …