Description

Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants

Input

name:type
description
pattern

meta{:bash}

:map

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

muse_call_txt{:bash}

:file

single input file generated by ‘MuSE call’

*.MuSE.txt

ref_vcf{:bash}

:file

dbSNP vcf file that should be bgzip compressed, tabix indexed and based on the same reference genome used in ‘MuSE call’

.vcf.gz

ref_vcf_tbi{:bash}

:file

Tabix index for the dbSNP vcf file

.vcf.gz.tbi

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:map

bgzipped vcf file with called variants

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:map

tabix index of bgzipped vcf file with called variants

*.vcf.gz.tbi

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

versions_bgzip{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bgzip{:bash}

:string

The tool name

bgzip --version | sed -n 's/bgzip (htslib) \([0-9.]*\)/\1/p'{: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

${task.process}{:bash}

:string

The process the versions were collected from

bgzip{:bash}

:string

The tool name

bgzip --version | sed -n 's/bgzip (htslib) \([0-9.]*\)/\1/p'{: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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