Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

tumor_file{:bash}

:file

Tumor or metastatic sample, BAM or CRAM file

*.{bam,cram}

tumor_file_bai{:bash}

:file

Index of BAM file

*.{bai,crai}

control_file{:bash}

:file

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

*.{bam,cram}

control_file_bai{:bash}

:file

Index of BAMfile

*.{bai,crai}

fasta{:bash}

:file

The reference fasta file

*.fa

fai{:bash}

:file

Index of reference fasta file

*.fai

skipregions_file{:bash}

:file

File with regions to skip, region as comma-separated list of chr:start-end, or just list of chr, or nothing

*.bed|*.txt|*.tab

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

Output VCF file

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

Index of VCF file

*.vcf.gz.tbi

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

Log file

*.log

version{:bash}

versions.yml{:bash}

:file

File containing software version

*.{version.txt}

Tools

maintainer
Github user kubranarci
get in touch
Ask a question on Slack Open an issue on GitHub