Question: How to find all the Somatic Mutations in a Chromosome
1
gravatar for mcc
3.1 years ago by
mcc80
PVD, USA
mcc80 wrote:

I want to produce a list of all the somatic mutations that are known using the 1000 genome project and using ensembl.  How do I start this project?

ADD COMMENTlink modified 3.1 years ago by Emily_Ensembl14k • written 3.1 years ago by mcc80
1

Maybe you mean COSMIC (catalogue of somatic mutations in cancer)?

ADD REPLYlink written 3.1 years ago by Irsan6.6k
4
gravatar for EnsemblWill
3.1 years ago by
EnsemblWill550
United Kingdom
EnsemblWill550 wrote:

While you could use BioMart or the API to retrieve these data, you might be better off with VCF file dumps:

ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/

Homo_sapiens_somatic.vcf.gz (all somatic mutations from COSMIC and dbSNP) and Homo_sapiens.vcf.gz (all non-somatic variants from various sources, see http://www.ensembl.org/info/genome/variation/sources_documentation.html ) from this directory should be a good place to start.

If you specifically only want those from the 1000 genomes project, you could grep for the 1000 genomes evidence flag:

curl ftp://ftp.ensembl.org/pub/release-79/variation/vcf/homo_sapiens/Homo_sapiens.vcf.gz | gzip -dc | grep E_1000G | head

or download the population-specific files from the above directory, or the VCF files from the original project site (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ ).

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by EnsemblWill550
2
gravatar for Emily_Ensembl
3.1 years ago by
Emily_Ensembl14k
EMBL-EBI
Emily_Ensembl14k wrote:

1000 Genomes only looked at germline variants. There are no somatic mutations in the 1000 Genomes Project.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Emily_Ensembl14k

Hi Emily,

Thank you for your response.  I acutally want to find the somatic mutation in Ensembl and compare them to the SNP mutations that appear in the 1000 Genome project.  

Can you steer me in the right direction that could help me with this task.  I was wondering if Ensembl has a tutorial to find all the somatic mutations for the first chromosome for example.

Thank You,

Matt

ADD REPLYlink written 3.1 years ago by mcc80
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