Hi, I'm doing some variant-calling, and I was wondering what is the difference between:
merging BAM files with samtools merge and call samtools mpileup on the merged BAM
skip the merge step and call mpileup with all the BAM files?
I did both and expected the same results, but I got 15% of identical SNPs, 60% close to identical but lower quality with the samtools merge step, and the others SNPs are not find by one or the other method.
Is it possible that the quality filter applied in mpileup affect each file separately and cause this behaviour or is it something else?