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Last pushed: a month ago
Short Description
Automated build for platypus-nf
Full Description

Platypus-nf

Germline variant calling with platypus

Description

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).

Dependencies

  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.

Input

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

Parameters

  • Optional

    | Name | Example value | Description |
    |------------------|-----------------------------|--------------|
    | --platypus_bin | /usr/bin/Platypus.py | 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
--optimized use optimized parameters: --badReadsThreshold=0 --qdThreshold=0 --rmsmqThreshold=20 --hapScoreThreshold=10 --scThreshold=0.99

Download test data set

  cd ~ && git clone https://github.com/iarcbioinfo/data_test

Usage

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

Output

Type Description
VCFs one VCF by input BAM

Directed Acyclic Graph

Contributions

Name Email Description
Tiffany Delhomme* delhommet@students.iarc.fr Developer to contact for support (link to specific gitter chatroom)
Docker Pull Command
Owner
iarcbioinfo
Source Repository

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