Effect of pooling and SNP calling on estimated site frequency spectrum (SFS). The thick black line depicts the true SFS after pooling, but before sequencing, i.e., as if power was 1 and no false discoveries. Boxplots show the estimated SFS after sequencing and SNP calling for reads with exact depth 20. The two best methods are compared: samtools mpileup and snape with informative prior. Results for 100 replicates and N = 100 chromosomes.