hannespetur/dipcall

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

Getting Started

wget https://github.com/lh3/dipcall/releases/download/v0.1/dipcall-0.2_x64-linux.tar.bz2
tar -jxf dipcall-0.2_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]

Output

The final output of dipcall includes two files: prefix.dip.vcf.gz and prefix.dip.bed. A raw variant call is made in the VCF if a non-reference allele is observed in any alignments >=50kb and mapped with mapping quality >=5. In the VCF, dipcall sets a HET1 filter if parent1 is a heterozygous at the raw variant; dipcall sets a GAP1 filter if no >=50kb alignment from parent1 covers the variant. Note that if a call is covered by multiple >=50kb alignments in the same parent but the alignments all have the same allele, the call is not filtered in the VCF.

The BED file gives the confident regions. A base is included in the BED if 1) it is covered by one >=50kb alignment with mapQ>=5 from each parent and 2) it is not covered by other >=10kb alignments in each parent. Nearly all calls filtered in the VCF are excluded in the BED, except very rare edge cases. However, a fraction of unfiltered calls in the VCF may also be excluded by the BED. The BED file applies more stringent filter.

The above is applied to autosomes and female chrX. For a male sample, parent1 is assumed to be the father and parent2 the mother. Dipcall treats PARs the same way as autosomes. However, outside PARs, dipcall filters out chrX regions covered by father contigs and filters out chrY regions covered by mother contigs. To make proper calls on sex chromosomes, users should hard mask PARs on the reference chrY.