TCGA Broad Institute curated variants

Question

[umn_bist]

I am using RNA-seq data available at TCGA to call variants and through cross-checking with the curated MAF files provided by Broad Institute, it seems that there are a couple variants that either I'm not getting and some that they're not getting.

I was curious if there is available documentation that Broad Institute provides that records they're pipeline/workflow to understand why I'm getting different results.

Answer 1

[Chris Miller]

• The metadata (SDRF/IDF) files should give information on the parameters and such used in the variant callers.

• If you're comparing them to the curated MAFs, it's unsurprising that you'd be missing some variants. After all, not all genes are expressed, so you'll be unable to call variants in those.

• The opposite problem (calls you're making not in the MAF) may be due to a host of factors, including sequencing artifacts or low-VAF calls that weren't readily detectable in the original DNA sequencing.