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.
-
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.
Type | Description |
---|---|
--input_folder | Folder containing BAM files |
--ref | Path fo fasta reference |
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 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 |
git clone https://github.com/iarcbioinfo/data_test
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
Type | Description |
---|---|
VCFs | one VCF by input BAM |
Name | Description | |
---|---|---|
Tiffany Delhomme* | delhommet@students.iarc.fr | Developer to contact for support (link to specific gitter chatroom) |