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}

tumor_file_bai:file

Index of BAM file

*.{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

vcf

meta:map

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

*.vcf.gz:file

Output VCF file

*.vcf.gz

tbi

meta:map

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

*.vcf.gz.tbi:file

Index of VCF file

*.vcf.gz.tbi

log

meta:map

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

*.log:file

Log file

*.log

version

versions.yml:file

File containing software version

*.{version.txt}

Tools

maintainer
Github user kubranarci
get in touch
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