variant-calling/README.md

README.md

Author: Yaqing Liu

Email: yaqing.liu@outlook.com

Last Updates: 25/04/2021

Requirements

• choppy
• Ali-Cloud
• Linux

Introduction

Variant calling pipeline from mapping to generating MAF files with three optional callers, i.e. TNseq, TNscope and Varscan2, for WGS and WES data.

Please carefully check the reference genome, bed file, etc.

Usage

open-choppy-env

choppy install YaqingLiu/variant-calling-latest

choppy samples YaqingLiu/variant-calling-latest --no-default
# sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2

choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project -l Label

# Query the status of all tasks in the project
choppy query -L Label | grep "status"