Description

Clair3 is a germline small variant caller for long-reads

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

bam:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai:file

BAM index file

*.bai

packaged_model:string

string containing the name of a prepackaged Clair3 model full list of models and their descriptions is provided at https://github.com/HKU-BAL/Clair3?tab=readme-ov-file#pre-trained-models

user_model:directory

directory containing Clair3 model files

platform:string

val in [‘hifi’,‘ont’, ‘ilmn’] to indicate pacbio, ONT, or illumina respectively

meta2:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

reference:file

reference fasta file

*.fasta

meta3:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

index:file

reference index file

*.fai

Output

name:type
description
pattern

vcf

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.{vcf,vcf.gz}

${prefix}merge_output.vcf.gz:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.{vcf,vcf.gz}

tbi

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.{vcf,vcf.gz}

${prefix}merge_output.vcf.gz.tbi:file

index for vcf files

*.{vcf.tbi,vcf.tbi.gz}

phased_vcf

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.{vcf,vcf.gz}

${prefix}phased_merge_output.vcf.gz:file

phased vcf

*.{vcf,vcf.gz}

phased_tbi

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.{vcf,vcf.gz}

${prefix}phased_merge_output.vcf.gz.tbi:file

index for vcf files

*.{vcf.tbi,vcf.tbi.gz}

gvcf

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.{vcf,vcf.gz}

${prefix}merge_output.gvcf.gz:file

gvcf file

*.{gvcf,gvcf.gz}

gtbi

meta:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.{gvcf.tbi,gvcf.gz.tbi}

${prefix}merge_output.gvcf.gz.tbi:file

index for gvcf file

*.{vcf.tbi,vcf.tbi.gz}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

clair3
BSD-3-clause

Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration.

github.com/HKU-BAL/Clair3 10.1038/s43588-022-00387-x
maintainer
Github user robert-a-forsyth
get in touch
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