I have single-cell RNA-Seq experiment with >1000 samples from the same individual. To get an idea of their genotype, I want to do a pseudo-bulk variant call where I merge the 1000+ BAM files into one and call variants from that. The problem I have is that Freebayes will give each sample from the merged VCF file a separate column rather than one “merged” column. I couldn’t find any options on Freebayes that ignore read groups.