How to read the GATK BaseRecalibration report

Question

[stephenn]

Hi everyone,

I use GATK to do SNP call.But the BaseRecalibration report confused me. what is reported quality scores and the empirical quality. what is the difference between them?

Thanks!

[Ashutosh Pandey]

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html

http://gatkforums.broadinstitute.org/discussion/44/base-quality-score-recalibration-bqsr