bcftools mpileup -f reference.fa positionsort.bam | bcftools call -mv -Ob -o calls.bcf
To my knowledge, bcftools mpileup ignores duplicates by default (here and here). Initially I assumed that this would be the same case for bcftools call. However, I was skeptical and decided to do a test where I variant call when I mark duplicates with Picard, and where I variant call without marking duplicates. To my surprise, this resulted in both cases in the exact same number of variants. So, does this mean that bcftools call doesn't ignore duplicate markings? Or have I made a mistake?
edit: I did in fact make a mistake, see comments below