Question: TCGA Broad Institute curated variants
0
gravatar for umn_bist
2.9 years ago by
umn_bist320
umn_bist320 wrote:

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.

rna-seq snv tcga broad institute • 1.0k views
ADD COMMENTlink modified 9 days ago by Biostar ♦♦ 20 • written 2.9 years ago by umn_bist320
1
gravatar for Chris Miller
2.9 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:
  • 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.

ADD COMMENTlink written 2.9 years ago by Chris Miller20k
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