I found similar questions here, but couldnt find exactly what I am searching for.
I have several (+180) .bam files, each from a different sample. I will proceed to SNP calling with SAMtools/bcftools. I need to obtain a single .vcf file with all my samples on it. Should I merge all my .bam files and do the SNP calling once, or should I do the SNP calling for each sample and then merge all the .vcf files?
Thanks in advance!