Description

pre-filtering and calculating position-specific summary statistics using the Markov substitution model

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

tumor_bam{:bash}

:file

Sorted tumor BAM file

*.bam

tumor_bai{:bash}

:file

Index file for the tumor BAM file

*.bai

normal_bam{:bash}

:file

Sorted matched normal BAM file

*.bam

normal_bai{:bash}

:file

Index file for the normal BAM file

*.bai

reference{:bash}

:file

reference genome file

.fasta

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.MuSE.txt{:bash}

:file

position-specific summary statistics

*.MuSE.txt

versions_muse{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

muse{:bash}

:string

The tool name

MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

muse{:bash}

:string

The tool name

MuSE --version | sed -e 's/MuSE, version //g' | sed -e 's/MuSE v//g'{:bash}

:string

The command used to generate the version of the tool

Tools

MuSE
https://github.com/danielfan/MuSE/blob/master/LICENSE

Somatic point mutation caller based on Markov substitution model for molecular evolution

bioinformatics.mdanderson.org/public-software/muse github.com/wwylab/MuSE 10.1101/gr.278456.123
included in
sarek
maintainer
Github user famosab
get in touch
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