Description

Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module.

Input

Name (Type)
Description
Pattern

meta (map)

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

reads (file)

Raw fastq files for one sample, single or paired end.

*.{fastq.gz}

meta2 (file)

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

snp_pt (file)

PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate’s github repository.

*.{pt}

Output

Name (Type)
Description
Pattern

meta (map)

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

vaf (file)

Text file containing reference/alt allele depth for each SNP position contained in the PT file.

*.{vaf}

versions (file)

File containing software versions

versions.yml
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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