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When to use BQSR?

snwilliams88snwilliams88 University of North Carolina at Chapel HillMember
edited May 2015 in Ask the GATK team


I am new to NGS/GATK & have a paired-end targeted (targeted to 1 region on 1 autosome) illumina sequencing project on roughly 470 samples. I was wondering whether Indel Realignment & BQSR were appropriate for my setting, or what considerations should be taken into account when judging whether these steps are appropriate?

I'm curious because I noticed this text here:
Small targeted experiments
The same guidelines as for whole exome analysis apply except you do not run BQSR on small datasets.

I was unsure whether my project qualified as a 'small dataset' where BQSR should not be run.

Thanks for any help you may be able to offer!


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