Clair - Yet another deep neural network based variant caller

Contact: Ruibang Luo
Email: rbluo@cs.hku.hk

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Introduction

This is Clair v1, which was made available in Jan 2019. Please visit v2, Nov 2019 for the latest version.

Clair is the successor of Clairvoyante.

Usage

git clone https://github.com/HKU-BAL/Clair.git
cd Clair
./clair.py

Models

Please download models from here.

Folder	Tech	Sample used	Depth used
pacbio/rsii	PacBio RSII	HG001,2,3,4	"Full depth of each sample" x {0.1,0.2,0.4,0.6,0.8,1.0}
pacbio/ccs	PacBio CCS 15k	HG002	~28-fold x {0.1, 0.2 ..., 0.9}
ont/r94	ONT R9.4 (no flip-flop)	HG001	~37-fold x {0.1, 0.2 ..., 0.9}
ont/r94-flipflop	ONT R9.4 (flip-flop)	HG001	~150-fold x 0.7{0,1 ..., 9}