Awesome
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
-
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.
-
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 | Description | |
|---|---|---|
| Tiffany Delhomme* | delhommet@students.iarc.fr | Developer to contact for support (link to specific gitter chatroom) |