Allows population indel detection and genotyping. piCALL detects and allows genotyping of small indels from population-scale sequence data. The software is compatible with data from different sequencing platforms but requires all samples to be sequenced using the same sequencing platform. The method requires sequence data from a sufficient number of samples to accurately estimate the population genotypes. Its performance was assessed using population sequencing data generated by the 1000 Genomes project (exon sequencing).