How To Get Ensembl Id (Gene, Transcript, Protein) Information?

Question

[mgab]

I have few VCF Files which contains Chromosome number, position, Variation allele (Ref and Alt).

How can I generate the Gene name, its Refseq and listing all of its transcripts? 1. Any tool which gives these kind of results when upload VCF data? 2. Is there any module in Biopython or Bioconductor or script for this? 3. Is there any lists that links gene name to Refseq and transcript information?

Thank you for the valuable suggestions

Answer 1

[memory_donk]

Ensembl BioMart is probably your best bet.

You may need to use/write a quick script or awk command to extract your chromosome number and position but you can enter a list of chromosomal positions in the filter menu under regions->multiple chromosomal positions. You can then choose which attributes you would like to download such as Ensembl Gene ID or (under the external references menu) Refseq id.

If your list is too long you'll probably have to use the Perl API. Short tutorial available here: http://www.ensembl.org/info/data/biomart/biomart_perl_api.html

[mgab]

Thank you for donk for the suggestion

Answer 2

[Emily]

You need the variant effect predictor, does exactly what you need.

[mgab]

Thank you for Emily for the suggestion