https://github.com/lh3/dipcall

Reference-based variant calling pipeline for a pair of phased haplotype assemblies
https://github.com/lh3/dipcall

Last synced: about 2 months ago
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Reference-based variant calling pipeline for a pair of phased haplotype assemblies

• Host: GitHub
• URL: https://github.com/lh3/dipcall
• Owner: lh3
• License: mit
• Created: 2019-10-03T03:29:52.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2021-06-06T20:36:10.000Z (over 3 years ago)
• Last Synced: 2024-11-16T05:32:06.029Z (about 2 months ago)
• Language: JavaScript
• Size: 23.4 KB
• Stars: 96
• Watchers: 4
• Forks: 10
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
## Getting Started

```sh

wget https://github.com/lh3/dipcall/releases/download/v0.3/dipcall-0.3_x64-linux.tar.bz2

tar -jxf dipcall-0.3_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][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.

[syndip]: https://github.com/lh3/CHM-eval