GATK v3.1 HaplotypeCaller with GATK 1.6 Realigned & Relcalibrated BAMs
For GATK v3.1 I want to use the HaplotypeCaller with Combine gVCFs & Genotype gVCFs on GATK 1.6 Realigned & Relcalibrated BAMs.
A) Should I realign and recalibrate my BAMs with GATK v3.1 prior to using the HaplotypeCaller?
Is this a problem for other issues I am not seeing?
C) Should I not go this route and just use UnifiedGenotyper to call variants jointly across all of my samples?
FYI - This is for a cohort of ~1000 germline exome samples.