pbsnp

Instruction

pbsnp is the pipeline of snps calling from pacbio reads by gatk4. If run it, following steps will execute:

minimap2 --> samtools sort --> MarkDuplicates --> gatk HC

Dependencies

Following is a list of thirty-party progams that will be used in pbsnp pipeline.

• minimap2
• gatk4 v4.0+
• picard
• samtools

Install

1. Download

git clone https://github.com/wangyibin/pbsnps.git

2. Configure

export PATH=/path-to-pbsnps:$PATH
export picard="/path-to-picard/picard.jar"

Usage

pacbio-snps-gatk4.sh test.fasta test.fq.gz test

or run with multithreads

pacbio-snps-gatk4.sh test.fasta test.fq.gz test 8

Reference

Comprehensive variant detection in a human genome with PacBio high-fidelity reads. William J. Rowell, Paul Peluso, John Harting, Yufeng Qian, Aaron Wenger, Richard Hall, David R. Rank. PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025.