SNPEFF_GENE_NAME annotates with accession numbers that are not intuitively mapped to a single field

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9.2 years ago

Ram 43k

The NGS pipeline at my facility uses snpEff to annotate variants, and the result VCF has the SNPEFF_GENE_NAME field. This field has as its values the accession numbers to records under NCBI Protein. However, the values in the field do not map to a single attribute of those records in a predictable/uniform fashion. Some map to the primary accession number, and others to one of the extra accessions.

How can I unify this? If I wished to replace the accession number with the name found on the Locus field (XYZ_HUMAN), how can I achieve that?

snpeff accession RNA-Seq • 1.8k views

ADD COMMENT • link 23 months ago by Ram 43k

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What snpEff database was used?

ADD REPLY • link updated 23 months ago by Ram 43k • written 9.1 years ago by Sean Davis 26k

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Hi Sean, I'll get back to you with the details as soon as I figure out how to find which database was used.

ADD REPLY • link 9.1 years ago by Ram 43k

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