Is there a GRCh37 equivalent of EnsDb.Hsapiens.v86 or some other method for getting a complete list of genes and their coordinates from GRCh37?
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5.6 years ago

I'm looking to work out if any of a large list of SNPs occur within the genomic range of any gene. The coordinates I have for the SNPs, however, are in GRCh37. I have the EnsDb.Hsapiens.v86 object in R, which provides a full list of genes and their genomic ranges, which is exactly what I need, however, all coordinates for the object are given in GRCh38. Is there an equivalent package/object for GRCh37? Or another method for mapping SNPs to the genes whose genomic ranges they occur within?

assembly genomics R bioconductor • 6.1k views
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Did you try Ensembl Biomart ?

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5.6 years ago

This version of the same package is the latest (last) release for GRCh37.

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Why thank you, sir!!

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5.6 years ago
vkkodali_ncbi ★ 3.7k

The last full annotation of GRCh37 by NCBI RefSeq was back in 2014. However, an interim annotation was run in 2017 and you can download those data in GFF3 format here: ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/GRCh37.p13_interim_annotation/

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5.6 years ago
Tm ★ 1.1k

You can also give a try to snpefff and Variant Effect Predictor.

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