Is it possible to pass multiple bams to GATK4 HaplotypeCaller?
Because of a variety of preprocessing steps that I have to perform on my input bam I have split it by chromosome to make this process faster. Joining these bams together before calling SNVs with HaplotypeCaller is a very time consuming step so it would be most convenient to just pass all the bams at once without the join. Is it possible to pass multiple bams to HaplotypeCaller? I have tried a variety of ways such as
gatk-launch HaplotypeCaller -R hg19-1.2.0/fasta/genome.fa -I example.20.bam -I example.21.bam -O out.vcf
and the Mutect2 way
gatk-launch HaplotypeCaller -R hg19-1.2.0/fasta/genome.fa -I:20 example.20.bam -I:21 example.21.bam -O out.vcf
Is this even possible?
Thanks very much,