BAQ and quality recalibration with GATK

[csoong]

Hi,
question on quality recalibration with GATK: would quality calibration occur before BAQ capping or after? Or does it matter?

Also, does anybody have experience on how much a difference would recalibration contribute to cleaning up the data in terms of snp calling and indel calling?

Thanks,
CSoong

[csoong]

I decided to run recalibration before BAQ. Anyway, the recalibrated bam files were like 50-75% larger than the original ones. Does anyone know why?

Thanks,
CSoong

[csoong]

perhaps due to uncompressed vs compressed?

[cheehongsg]

I decided to run recalibration before BAQ. Anyway, the recalibrated bam files were like 50-75% larger than the original ones. Does anyone know why?

Thanks,
CSoong

The original quality string is kept + the recalibrated quality string, so it will be larger.

[csoong]

thx for the input; that makes sense. i thought it just edits the original quality scores instead of adding the recal scores.