Variant Calling

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

Supported callers

All callers are not activated by default, which means the default setting is false. You need to manually set the caller to true in the submitted sample.csv. The fields corresponding to these callers include haplotyper, tnseq, tnscope, varscan.

Germline

• Haplotyper

If you only want to call germline variants, please set haplotyper to true.

Somatic

• TNseq (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• TNhaplotyper (This caller is only available in v0.1.0 as it is too outdated)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 for somatic variant calling
• TN matched WGS for somatic variant calling
• Normal-only WES for germline variant calling
• Normal-only WGS for germline variant calling

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

New Releases

• The TNhaplotyper, named as TNseq in v0.1.0, has beed substituted by TNhaplotyper2.
• The corealigner step has been removed.
• The vcf2maf step has been removed. Thus, the final output is the annotated VCF.

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