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

meta1 (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

bowtie_index (directory)

Folder of Bowtie genome index files

Output

Name (Type)
Description
Pattern

meta1 (map)

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

versions (file)

File containing software versions

versions.yml

pt (file)

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

*.pt
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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/NGSCheckMate10.1093/nar/gkx193