How to properly merge bamouts after Mutect2
I ran Mutect2 (gatk4) using the -L command to split by chromosome, and the -bamout option.
I am now using CatVariants (gatk3) to merge all the vcf files (one per chr) into a final vcf.
And I also need to merge the bamouts. I know there are several tools to merge bams, but I've read that some of such tools have issues with the headers, etc.
Is there any particular tool you would recommend to properly merge the bams?