Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data.

References:

• Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R. F. Twigg, WGS500 Consortium, Andrew O. M. Wilkie, Gil McVean, Gerton Lunter. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nature Genetics (2014) doi:10.1038/ng.3036

• Platypus main site

• Module Name: platypus (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --gres lscratch:1
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOBID
[user@cn3144 46116226]$ module load platypus
[+] Loading platypus, version 0.8.1...
[user@cn3144 46116226]$ platypus callVariants \
> --bamFiles /fdb/app_testdata/bam/hg19/gcat_set_053.bam \
> --refFile /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa \
> --output gcat_set_053.vcf 
2017-09-29 14:53:42,435 - INFO - Beginning variant calling
2017-09-29 14:53:42,435 - INFO - Output will go to gcat_set_053.vcf
2017-09-29 14:53:42,710 - INFO - Processing region chr1:0-100000. (Only printing this message every 10 regions of size 100000)
2017-09-29 14:53:43,061 - INFO - Processing region chr1:1000000-1100000. (Only printing this message every 10 regions of size 100000)
...
...
2017-09-29 15:04:50,820 - INFO - Processing region chrY:58300000-58400000. (Only printing this message every 10 regions of size 100000)
2017-09-29 15:04:51,941 - INFO - Processing region chrY:59300000-59373566. (Only printing this message every 10 regions of size 100000)
2017-09-29 15:04:51,947 - INFO - Merging output VCF file(s) into final file gcat_set_053.vcf
2017-09-29 15:04:55,587 - INFO - Finished merging VCF file(s)
2017-09-29 15:04:55,591 - INFO - Finished variant calling
[user@cn3144 46116226]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. platypus.sh). For example:

#!/bin/sh

set -e
module load platypus

platypus callVariants \
 --bamFiles /fdb/app_testdata/bam/hg19/gcat_set_053.bam \
 --refFile /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa \
 --output gcat_set_053.vcf

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] platypus.sh

Create a swarmfile (e.g. platypus.swarm). For example:

platypus callVariants --bamFiles input1.bam --refFile hg19.fa --output input1.vcf
platypus callVariants --bamFiles input2.bam --refFile hg19.fa --output input2.vcf
platypus callVariants --bamFiles input3.bam --refFile hg19.fa --output input3.vcf
platypus callVariants --bamFiles input4.bam --refFile hg19.fa --output input4.vcf

Submit this job using the swarm command.

swarm -f platypus.swarm [-g #] [-t #] --module platypus