Hi Folks, I just want to make sure I am on the right track. I have paired reads coming from three Lanes per each sample. Following is what I did so far; I mapped reads to reference genome using BWA in SAM tools.
Now I have indexed BAM files (3 per each sample).
I am thinking of merging bam files using Sam tools and then go for Variant calling.
I read that alternatively, variants can be called for each indexed bam file and then merge vcf files.
What is the more logical approach? Looking forward to get your suggestions. Thank you! 🙂