How to analyze DNA data with UMI

Question

[deniselavezzari]

Hi all!

I'm facing with analyze DNA exomes sequencing data with UMI. From the demultiplexing, I have three fastq files: one for reads R1, one for the UMI tags, and one for the R2. Now, I have to align data to the reference genome and call variants. Have you some suggestions for me?

Does anyone know some "best practices" for that?

Thanks
Denise

[ATpoint]

Have you looked at documentation of standard software such as UMI-tools?

Also, see How to take in consideration UMI in WES pipeline?. By the way, Ian (the guy who answers this question) is the author of UMI-tools.