Public | Automated Build

Last pushed: 6 days ago
Short Description
Automated build for platypus-nf
Full Description


Germline variant calling with platypus


Perform germline variant calling with platypus, with optional use of optimized parameters based on performance analysis on Illumina Platinium Genome (both whole exome/genome sequencing).

The platypus nextflow pipeline can also add a step to the variant calling:

  • compress (bgzip) and index (tabix). These two tools are part of the samtools/htslib C library, see documentation for the installation.


  1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.

  2. Platypus: see official installation here. You can avoid installing all the external software by only installing Docker. See the IARC-nf repository for more information.


Type Description
--input_folder Folder containing BAM files
--ref Path fo fasta reference


  • Optional

    | Name | Example value | Description |
    | --platypus_bin | /usr/bin/ | path to platypus executable |
    | --region | chr1;chr1:0-1000; mybed.bed | region to call |
    | --cpu | 12 | number of cpu used by platypus |
    | --mem | 4 | memory in GB used by platypus |
    | --output_folder | . | folder to store output vcfs |
    | --options | " --scThreshold=0.9 --qdThreshold=10 " | options to pass to platypus |
  • Flags

Flags are special parameters without value.

Name Description
--help Display help
--compression compress and index the VCF file
--filter output only PASS variants
--optimized use optimized parameters: --badReadsThreshold=0 --qdThreshold=0 --rmsmqThreshold=20 --hapScoreThreshold=10 --scThreshold=0.99

Download test data set

  git clone


  nextflow run iarcbioinfo/platypus-nf -with-docker --input_folder data_test/BAM/ --ref data_test/REF/17.fasta


Type Description
VCFs one VCF by input BAM

Directed Acyclic Graph


Name Email Description
Tiffany Delhomme* Developer to contact for support (link to specific gitter chatroom)
Docker Pull Command
Source Repository