GATK 3 to GATK 4 and BQSR
I am trying to modify my exome pipelines to integrate GATK4.
For the recalibration, I used with GATK 3 two round of BaseRecalibrator and used the recalibration table in happlotype caller with -BQSR option in order to avoid writing intermediate bam files that are a lot bigger.
With the new GATK it does not seems to be possible to do 2 round and use the recalibrate table for the haplotype caller. Is the -BQSR option still available in the new happlotyecaller.
Thanks for your help.