ICAPGen

ICAPGen is a bioinformatics software package designed to assist researchers in genotyping and genotype imputation from high-throughput sequencing and array data. Developed by teams affiliated with the ICAP consortium, the tool aims to streamline the generation of high-confidence genotype calls and phased haplotypes for large cohorts. ICAPGen supports standard genomic data formats, including VCF for variant data and BAM/CRAM for aligned reads, and it can integrate with reference panels to improve imputation accuracy.

Key features include genotype calling, haplotype phasing, imputation, and quality control reporting. It emphasizes scalability, offering parallel processing and efficient memory use to handle large population studies. Output typically includes annotated VCF files with phased genotypes, genotype probabilities or likelihoods, and summary QC metrics. The interface is primarily command-line based, with configuration options to fit into automated analysis pipelines, and it has been reported to interoperate with common workflow systems and downstream tools.

ICAPGen is distributed as open-source software under a permissive license and is maintained through community contributions and periodic releases. Documentation covers installation, data preparation, parameter selection, and examples of integration into end-to-end genomic analysis pipelines. The tool is used in academic research on population genetics, association studies, and clinical genomics, where reliable genotype data and haplotype information are essential.