Description

Platypus is a tool that efficiently and accurately calling genetic variants from next-generation DNA sequencing data

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

tumor_file (file)

Tumor or metastatic sample, BAM or CRAM file

*.{bam,cram}

tummor_file_bai (file)

Index of BAMfile

*.{bai,crai}

control_file (file)

Control (or blood) of matching tumor/metastatic sample, BAM or CRAM file

*.{bam,cram}

control_file_bai (file)

Index of BAMfile

*.{bai,crai}

fasta (file)

The reference fasta file

*.fa

fai (file)

Index of reference fasta file

*.fai

skipregions_file (file)

File with regions to skip, region as comma-separated list of chr

, or just list of chr, or nothing

*.bed|*.txt|*.tab

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

vcf (file)

Output VCF file

*.vcf.gz

tbi (file)

Index of VCF file

*.vcf.gz.tbi

log (file)

Log file

*.log

version (file)

File containing software version

*.{version.txt}
maintainer
Github user kubranarci
get in touch
Ask a question on Slack Open an issue on GitHub

Tools