You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
YaqingLiu
b76c7f072f
Update: deduped_Matrics
|
4 anni fa | |
|---|---|---|
| .vscode | 4 anni fa | |
| tasks | 4 anni fa | |
| .DS_Store | 4 anni fa | |
| LICENSE.md | 4 anni fa | |
| README.md | 4 anni fa | |
| defaults | 4 anni fa | |
| inputs | 4 anni fa | |
| workflow.wdl | 4 anni fa | |
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"