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9 months ago
hkarakurt
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180
Hello everyone,
I am working on genomic variants and their effects on proteins. I need to find how amino acid sequence of altered protein changes with a variant. Is it possible to annotate the VCF file or variant with HGVS format.
Thank you in advance.
take a few minutes to search biostars.org for snpEff, vep . Furthemore review all your previous questions and add a comment or validate the answers (green tick on the left) if needed: Using Specific Regions of Genome as Reference for Alignment Using STAR Weighted gene regulatory networks A method to find if a variant is Genomic or an RNA-Editing variant Using DESeq2 as one sample vs. population Formula for Differential Expression Analysis of 2 conditions and 2 cell types Oxford Nanopore Variant Calling Pipeline Calls Very Few of Variants of NA12878 Normalization and Batch Effect of bulk RNA-Seq Genomic Variant calling from RNA-Seq Data Using Seurat 3 Data for Pseudotime Analysis in Monocle 3 Calculating GC content around a specific genomic location Trimmomatic trims most of the reverse strand SNPs on a single transcript of a gene with multiple transcripts Network Analysis of Each Cluster of Protein Interaction Network Using FPKM and TPM values for batch correction for Single Cell RNA-Seq Automatic Coloring for Each Node According to Names in Cytoscape Differential Expression Analysis between conditions of single cell RNA-Seq Mitochondrial Gene percentage threshold in single cell RNA-Seq Enrichment Analysis with only GeneSymbols Hisat2 or Bowtie2 for ChIP-Seq Data? Genes with promoter and enhancer regions as GTF Differential ChIP-Seq Analysis How to extrach gene names and peaks from BedGraph or BigWig files Deseq2 results have too many genes Cufflinks gives only CUFF names with a gtf. Expression data extraction error. Logical result as expression matrix Retrieving data from NCBI GEO and RNA-Seq Data Analysis Tool for predicting transcription factors from a gene list How to extract expression data from RAW data.
Looks like Ensembl VEP can do that: https://github.com/Ensembl/ensembl-vep