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:map

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

bed:file

BED file containing population-level SNPs to use

*.bed

meta2:map

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

fasta:file

Genome fasta file

*.fasta

meta3:map

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

bowtie_index:directory

Folder of Bowtie genome index files

Output

name:type
description
pattern

pt

meta:map

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

*.pt:file

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

*.pt

versions

versions.yml:file

File containing software versions

versions.yml

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
Github user sppearce
Ask a question on Slack Open an issue on GitHub