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

vaf

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

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