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GATK usage for Targetted Exome sequencing data analysis

AswathyNAswathyN BangaloreMember

We are using a licensed version of GATK here.
The version is GATK version -2014.3-3.2.2-7-g f9cba99.

While using the tool for analysis of exome data I had few questions.

1: Are there different parameters used in GATK at different stages for whole and targeted exom sequencing data ?

2: What are the guidelines being followed for targeted exome seq analysis if I use BQSR ?

I was reading the page ("https://www.broadinstitute.org/gatk/guide/tagged?tag=exome") and it was mentioned as " The same guidelines as for whole exome analysis apply except you do not run BQSR on small datasets."

Request you to kindly clear the doubts.


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