Description

Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information about the bed file e.g. [ id:'test', single_end:false ]

bed{:bash}

:file

BED file containing population-level SNPs to use

*.bed

meta2{:bash}

:map

Groovy Map containing sample information about the fasta genome e.g. [ id:'test', single_end:false ]

fasta{:bash}

:file

Genome fasta file

*.fasta

meta3{:bash}

:map

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

bowtie_index{:bash}

:directory

Folder of Bowtie genome index files

Output

name:type
description
pattern

pt{:bash}

meta{:bash}

:map

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

*.pt{:bash}

:file

Generated binary pattern file, containing FASTQ strings to match from within raw data

*.pt

versions_ngscheckmate{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

ngscheckmate{:bash}

:string

The tool name

ncm.py --help | sed '7!d;s/.* 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

ngscheckmate{:bash}

:string

The tool name

ncm.py --help | sed '7!d;s/.* v//g'{:bash}

:string

The command used to generate the version of the tool

Tools

ngscheckmate
MIT

NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA.

github.com/parklab/NGSCheckMate 10.1093/nar/gkx193
maintainer
Github user sppearce
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