variant-calling/README.md

Variant Calling

This APP developed for somatic short variant discovery (SNVs + Indels).

Supported callers

• TNhaplotyper2
• TNscope
• VarScan
• TNhaplotyper (This caller is only available in v0.1.0 as it is too outdated)

Variant caller can be selected by setting ture/false in the submitted sample.csv.

Accepted data

• TN matched WES
• TN matched WGS

The datatype is judged by whether the bed file is set (i.e. the regions in inputs).

New Releases

• The TNhaplotyper, also named as TNseq in v0.1.0, has beed substituted by TNhaplotyper2.
• The corealigner step has been removed.

Getting Started

We recommend using choppy system and Aliyun OSS service. The command will look like this:

# Activate the choppy environment
$ open-choppy-env

# Install the APP
$ choppy install YaqingLiu/variant-calling-latest [-f]

# List the parameters
$ choppy samples YaqingLiu/variant-calling-latest [--no-default]

# Submit you task with the `samples.csv file` and `project name`
$ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label]

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

Please note: The defaults can be forcibly replaced by the settings in samples.csv. Therefore, there is no need to contact me over this issue.

The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2

Please carefully check

• the reference genome
• bed file
• the caller you want to use
• whether PoN needs to be set