Does bcftools call ignore duplicate markings?

Does bcftools call ignore duplicate markings?

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I am using Picard MarkDuplicates to mark duplicates in my position sorted BAM. Then, I variant call using bcftools mpileup and bcftools call like so:

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?


samtools


ignore


bcftools


markings


duplicates

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