WES allelic imbalence

Question

[SurdanBurasi]

Hello friends

I'm working on whole exom sequencing. however, I need allelic imbalance data to show how accurate my work is. How can I produce AB data?

my pipeline is:

bcl2fastq -> bwa -> gatk (best practise) -> ensembl-vep

Answer 1

[prasundutta87]

Why are you testing for allelic imbalance using exome (DNA-seq) data? You only use DNA-seq data for genotyping sites and get high-quality heterozygous sites and then use expression (RNA-seq) data from the same organism on those sites to get allelic imbalance results.

You can get a good understanding on the concept of allelic imbalance or allele-specific expression from this paper:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0762-6