Variant Calling

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

Accepted data

• TN matched or tumor-only WES/WGS for somatic variant calling
• Normal-only WES/WGS for germline variant calling

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

• Both FASTQ and BAM data are acceptable.
• Please set the parameter input_fastq to true when the input is FASTQ, or set the parameter input_bam to true when the input is BAM.

Supported variant callers and annotation tools

• Variant calling: haplotyper, pindel (germline); tnseq, tnscope, varscan (somatic; varscan don’t support the variant calling of tumor-only data).

• Annotation: annovar, vep.

• The above tools 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.

New Releases

• Two annotation tools have been added.
• TNhaplotyper, named as TNseq in v0.1.0, has beed substituted by TNhaplotyper2.
• The corealigner step has been removed.
• Some parameters’ details have been changed, such as the interval_list has turned into interval.

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 [-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 project: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 you want to use is hg38 or hg19.
• bed file.
• the caller you want to use.
• PoN VCFs for TNseq and TNscope is supported, but are need to be generated in advance.
• interval padding is default 0, and you can change it.
• usually only one annotation tool is sufficient.