bcftools mpileup before bcftools call

Question

[Egelbets]

I want to variant call using bcftools call. However, when researching, I see a lot of people running bcftools mpileup before doing the actual variant calling with call. For example (from here):

bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf

Could someone explain to me why this is done? I also don't understand what is meant with "mpileup generates genotype likelihoods at each genomic position with coverage"

Answer 1

[Istvan Albert]

The answer is exactly what you quoted, though the instructions could be more explicit.

A variant is simply a base with multiple, reasonably likely alternatives.

To find what varies we need to look at "every" base. Thus the 'pileup' will generate the likelihood at every base out of which the "call" decides which base passes the various thresholds and quality measures.