Cosmic Database using BioMart
1
0
Entering edit mode
4.0 years ago
noeD ▴ 100

Hello!

I have read that with BioMart package in R it is possible to download the cosmic database. Unfortunately I didn't understand how to do it. If I use listMart() I see only ensemble-database.. I have tried with listMart(host=http://cancer.sanger.ac.uk/cosmic), but it didn't work...

Thank you in advance for you help

Best

R BioMart Cosmic • 1.9k views
ADD COMMENT
4
Entering edit mode
4.0 years ago

You use the Ensembl variation somatic variation database to access COSMIC data:

cosmicMart = useEnsembl (biomart="snp", dataset = hsapiens_snp_som")

If you're looking to download the whole COSMIC database, BioMart is not a suitable way to do this. Please download the somatic VCF files from the FTP site instead: ftp://ftp.ensembl.org/pub/current_variation/vcf/homo_sapiens/

ADD COMMENT
0
Entering edit mode

Thank you for your reply. But is it possible to download the database for INDEL mutations?

Thank you in advance

ADD REPLY
0
Entering edit mode

You might be best downloading the VCF then using vcf-tools to filter

ADD REPLY

Login before adding your answer.

Traffic: 1540 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6