Question: 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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gravatar for SpacemanSpiffo
12 months ago by
SpacemanSpiffo10 wrote:

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?

ADD COMMENTlink modified 12 months ago by toralmanvar820 • written 12 months ago by SpacemanSpiffo10

Did you try Ensembl Biomart ?

ADD REPLYlink written 12 months ago by lakhujanivijay4.6k
2
gravatar for jared.andrews07
12 months ago by
jared.andrews074.1k
St. Louis, MO
jared.andrews074.1k wrote:

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

ADD COMMENTlink modified 12 months ago • written 12 months ago by jared.andrews074.1k

Why thank you, sir!!

ADD REPLYlink written 12 months ago by SpacemanSpiffo10
1
gravatar for vkkodali
12 months ago by
vkkodali1.5k
United States
vkkodali1.5k wrote:

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/

ADD COMMENTlink written 12 months ago by vkkodali1.5k
0
gravatar for toralmanvar
12 months ago by
toralmanvar820
toralmanvar820 wrote:

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

ADD COMMENTlink written 12 months ago by toralmanvar820
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