When to use BQSR?
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!