Broad Institute TCGA MAF procedure
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5.0 years ago
umn_bist ▴ 380

I am calling snv and indels on tumor/matched normal RNA-seq data from TCGA using Mutect2.

I am cross-validating with the curated MAF file by Broad, available at TCGA, but I was curious to know what sort of validation/QC/filtering steps they go through as a lot of their variants are not showing up in my raw/filtered vcf file.

Is there any documentation of their pipeline/workflow at TCGA?

RNA-Seq SNV MAF TCGA • 1.7k views
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