Any software that calculates the variant coordinates of a multi-exon deletion in a gene?

There are several software tools that can be used to calculate the variant coordinates of a multi-exon deletion in a gene. One example is ANNOVAR, which is a widely-used software tool for annotating genetic variants. ANNOVAR can be used to identify and characterize deletions in a gene, including multi-exon deletions. Other software tools that can be used for this purpose include Ensembl Variant Effect Predictor (VEP), which is a web-based tool for annotating the effects of genetic variants, and GeneWise, which is a software tool for predicting the effects of genetic variants on protein structure and function. It is also possible to use custom scripts or programming languages, such as Python or R, to calculate variant coordinates and annotate the effects of genetic variants.

Kristi Aleksi

Hi, Hevar Neaz.

Thank you for your prompt response.

I am acquainted with some of the websites you have suggested.

Only today could I find the link to this feature, which serves as the clearest illustration of what I'm searching for: https://databases.lovd.nl/shared/scripts/readingFrameChecker.php?gene=DMD&transcript=NM_004006.2

Not only does it check the reading frame for exonic deletions/duplications of the DMD gene but it also offers variants’ HGVS notation; I’m looking for something comparable to apply to other genes as well (as long as their transcript is provided).

Anyway, I’m downloading Annovar just to explore it a bit; it may come in handy eventually. I’m still trying to manage Ensembl, and, as for Python, I barely know the basics.

Regards.

Mohammad Alzeyadi

Hello.

There are several software programs and web-based tools that can help you convert nominal data of a multi-exon deletion into DNA coordinates in HGVS nomenclature, which is the standard notation for describing genetic variations.

ANNOVAR: This is a popular command-line tool that can annotate genetic variations in a variety of genomes, including the human genome. It can take raw variant data in VCF or BED format and output the coordinates in HGVS nomenclature, as well as functional predictions and conservation scores. You can use ANNOVAR to annotate multi-exon deletion variants in the NSD1 and NFIX genes.

VCF2HGVS: This is a Python script that can convert VCF files to HGVS notation. It can handle multi-exon deletions and insertions, as well as complex structural variations. It can also give you amino acid changes that result from the variants

HGVS Variation Nomenclature Mutation Converter: This is a web-based tool that can convert a variety of genetic variation notations, including HGVS, into HGVS nomenclature. It is also possible to convert multiple variants at once, including multi-exon deletions and insertions.

HGVS Variant Validator: This is a web-based tool that can validate the accuracy of HGVS notation, including multi-exon deletions and insertions.

vep (variant effect predictor): This is a command line tool that runs on a local machine and can help you identify the consequence of variants, such as SNPs, insertions, deletions on the genome, transcript and protein level. it can also output the HGVS notation of the variants.

It's important to note that these programs and web-based tools are designed to be used with raw sequence data and you need to have certain level of bioinformatics expertise to use them. If you are not familiar with bioinformatics, consider consulting with bioinformatician or researcher who have experience in working with variant calling, HGVS notation and NGS data in general.

In summary, there are several software programs and web-based tools that can help you convert nominal data of a multi-exon deletion into DNA coordinates in HGVS nomenclature, including ANNOVAR, VCF2HGVS, HGVS Variation Nomenclature Mutation Converter, HGVS Variant Validator, and vep. These tools can be used to analyze the NSD1 and NFIX genes.

Regards.

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