Validate mutations from WGS using RNA-seq bam files in IGV?

Question

[lincaijin1994]

Hi.

I've read a paper titled "A genomic and epigenomic atlas of prostate cancer in Asian populations" and it stated that " the missense mutations were validated by looking at RNA-seq BAM files in the IGV browser" in the supplemental information. But it didn't provide specific validation criteria.

If I want to validate mutations detected by WES, I'm wondering if the mutated reads >1 in the RNA-seq bam means a successful validation.

Thanks.

Lin.

[Arup Ghosh]

The authors have mentioned using two approaches for validation. Although they have not mentioned the exact criteria for the RNA-seq based approach, the respective validation datasets are available in http://www.cpgea.com/FOXA1_Mutation.php .

Two independent methods were used to validate FOXA1 mutations: Sanger sequencing and RNA-seq data.