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8.0 years ago
umn_bist
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390
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?