wget https://github.com/lh3/dipcall/releases/download/v0.1/dipcall-0.1_x64-linux.tar.bz2 tar -jxf dipcall-0.1_x64-linux.tar.bz2 # for female dipcall.kit/run-dipcall prefix hs38.fa pat.fa.gz mat.fa.gz > prefix.mak # or for male, requiring PAR regions in BED # dipcall.kit/run-dipcall -x dipcall.kit/hs38.PAR.bed prefix hs38.fa pat.fa.gz mat.fa.gz > prefix.mak make -j2 -f prefix.mak
Dipcall is a reference-based variant calling pipeline for a pair of phased haplotype assemblies. It was originally developed for constructing the syndip benchmark dataset and has been applied to other phased assemblies, too. Dipcall can call small variants and long INDELs as long as they are contained in minimap2 alignment.
If you use dipcall, please cite
Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D (2018) A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat Methods, 15:595-597. [PMID:30013044]