Anyone knows mutation pipeline for cbioportal?

Question

[fenghc]

Any reference that can explain how the cbioportal did gene mutation analysis? Thanks.

[fenghc]

Thanks a lot igor... Any comments on VCF files on https://gdc-portal.nci.nih.gov? How to compare custom mutation data with TCGA dataset?

[ivivek_ngs]

put it as another question and then you have to be clear what you intend to do? do you want to compare your mutational co-ordinates of your vcf file to that of the tcga mutation files? In that case you need to download the MAF file for particular cancers from tcga , exctract the coordinates and compare the postion of your vcf to that of the MAF with vcf tools or vcf-lib. Or you have to download from the gdc all the vcf file for a particular cancer, make a master vcf having all mutations, probably in your case overlapping and then compare the master vcf to that of your own vcf for the similar mutations.

[dago]

question not tool....

[WouterDeCoster]

You are right, but that's not an obvious tag (for new users). It now took 2 hours, but soon enough a moderator will come online to fix the post type so there is no need to become annoyed by that.

Answer 1

[igor]

cBioPortal takes the variant calls from the projects that they host. They just perform their own annotation for consistency.

The TCGA provisional datasets are directly from TCGA data center partly via Broad Firehose which are updated regularly. We are also actively curating datasets from literature. Studies from literature were curated from the data published with the papers. We sometimes reach out to the investigators to additional data such as clinical attributes. All the mutation data (VCF or MAF) were processed through an internal pipeline to annotate the variant effects in a consistent way across studies.

http://www.cbioportal.org/faq.jsp