Bioinformatics Asked by Nereus on June 8, 2021
I would like to create a list (probably .vcf format would be good) of all known pathogenic missense mutations in a human gene of interest and then add other variants that could lead to the same pathogenic amino acid substitutions. I intend to search targeted sequencing data of my gene of interest for variants that would cause these particular substitions.
I’m very new to bioinformatics so I’m not so familiar with the appropriate databases and tools to use, but this is a rough idea of how it could be done:
HGMD_MUTATION
(is there an option to download a vcf file with all HGMD mutations within my gene? I’ve only managed to do so for individual mutations.)Could you point me towards the best tools to use for these purposes? Unfortunately I haven’t got a HGMD subscription. Many thanks!
I'm not sure how to generate the additional mutations, but I would say that HGMD is not the way to find all the pathogenic variants. I would probably filter this table by either Clinical significance or Evidence->Phenotype association.
Answered by Emily_Ensembl on June 8, 2021
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