This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Where Can I Find Data Setnormal\Tumor Of Cancer?

Hi everyone! i want to run joint snvmix or var scan software for detection of somatic mutation in normal\tumor paired data,but i dont have any data to run it, if there is no data, can i simulate data ?

data cancer somatic mutation
• 3,794 views • link
updated by Kevin Kevin • written by mehrdadk.67 • mehrdadk.67

More information on what you're trying to accomplish would be helpful. TCGA is a great place to grab data, as mentioned below. Simulated data may or may not be a good soulution, depending on how well it represents real data. (Does it include normal admixture? altered ploidy and CN events? a specific mutation spectrum due to carcinogens, etc?)

• 232 views • link
written by Chris Miller Chris Miller

2 answers

Assuming you are in an academic institution you should be able to get TCGA data, although the access request will need to come from your PI.

https://cghub.ucsc.edu/access/get_access.html

Alternatively you could download synthetic data that has been made available for the recent DREAM challenge:

https://www.synapse.org/#!Synapse:syn2280639

• 153 views • link
written by hardingnj hardingnj

Other possible sources which have other kinds of datasets

European Genome-phenome Archive https://www.ebi.ac.uk/ega/datasets EGAD00001000082 20 Matched Pair Breast Cancer Genomes Illumina HiSeq 2000, Illumina Genome Analyzer II 42 bam https://www.ebi.ac.uk/ega/datasets/EGAD00001000082

https://discover.repositive.io/

• 0 views • link
written by Kevin Kevin

Log in to answer this question.

More posts like this