TCGA database call SNP

Question

[Michelle]

In TCGA, what's their quality control and criteria to define which is SNP?

Is it possible to know AWG's and GSC's data analysis procedure and filter?

[Cyriac Kandoth]

Please read this tutorial and all the comments below it - Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)

Answer 1

[Cyriac Kandoth]

I assume you mean somatic point mutations found in the TCGA MAFs? The term "SNP" refers to single nucleotide polymorphisms, usually used to refer to germline variations. TCGA uses the term SNV (Single Nucleotide Variant) to avoid confusion.

The somatic mutation calling methods used by the TCGA GSCs (Genome Sequencing Centers) or AWGs (Analysis Working Groups) have evolved a lot over the years. Sensitivity/specificity of the calls will differ between tumor-types, but is generally consistent across samples of the same tumor-type - Two known exceptions are OV and COAD/READ where multiple GSCs performed sequencing and/or variant calling.

WashU makes it's code public, so skimming through the POD of this module might give you some insight into their latest workflow. But in general, I would recommend reading the method's section of each marker paper listed here.

[Michelle]

Thanks, that helps a lot