I have 8 bam files ( obtained from 8 isolates from same species) and need to call variants. In order to get a final more confident SNP set I have decided to call variants using 5 different SNP callers and finally to get their intersect and filter appropriately.
One such tool I selected is Samtools mpileup. Although this tool is capable of multi-sample SNP calling, due to my limited memory capacity I'm unable to run them all together. My question is, If I call SNPs independently for each sample and later combine the 8 vcfs using (e.g. vcf-merge) would this course any issue in downstream analysis?
Appreciate your advices.
Best Regards Rangi