README.md

Author: Yaqing Liu

Email: yaqing.liu@outlook.com

Last Updates: 23/04/2021

Requirements

• choppy
• Ali-Cloud
• Linux

Introduction

This APP is used to

• convert a FASTQ file to an aligned BAM file.
• QC the data at the level of FASTQ and BAM, based on FastQC, FastQ Screen and Qualimap.

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

Usage

open-choppy-env

choppy install YaqingLiu/cbcga-wes-qc-latest

choppy samples YaqingLiu/cbcga-wes-qc-latest --no-default
# sample_id,fastq_1,fastq_2

choppy batch YaqingLiu/cbcga-wes-qc-latest samples.csv -p Project -l Label

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