Broad Institute TCGA MAF procedure
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?
• 2,614 views
•
link
written
by
umn_bist •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to identify biallelic mutations called using WES data?
written by tanbiswas6 •
-
Novogene somatic results with GATK mutect2
written by chrisgr •
-
Somatic variant calling with/without matched normal sample (Mutect2)
written by newbio17
-
Variant calling on matched primary and metastatic tumor without normal samples.
written by Venados •
-
TCGA Broad Institute curated variants
written by umn_bist •
-
TCGA tumor/normal RNA-seq somatic mutation calling
written by umn_bist •
-
Conceptual question regarding retrotransposon (RNA-seq) analysis
written by umn_bist •
-
TCGA: Bash assigning a tumor to its match normal
written by umn_bist •
-
Request to validate my RNAseq workflow
written by umn_bist •
-
Pipeline for >100 RNA-Seq PE samples
written by umn_bist •
