GATK 3 to GATK 4 and BQSR

wcarrewcarre RoscoffMember

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.


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