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Reference-based variant calling pipeline for a pair of phased haplotype assemblies
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README.md

Getting Started

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

Introduction

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]

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