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).

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.

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
--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 https://github.com/iarcbioinfo/data_test

Usage

With Docker:
nextflow run iarcbioinfo/platypus-nf -profile docker --input_folder data_test/BAM/ --ref data_test/REF/17.fasta
 
With Singularity
nextflow run iarcbioinfo/platypus-nf -profile singularity --input_folder data_test/BAM/ --ref data_test/REF/17.fasta

With Conda
nextflow run iarcbioinfo/platypus-nf -profile conda --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)