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 combined set of files e.g. [ id:'combined' ]

vafs:file

Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq

*.{vaf}

Output

name:type
description
pattern

pdf

meta:map

Groovy Map containing sample information about the combined set of files e.g. [ id:'combined' ]

*.pdf:file

A pdf containing a dendrogram showing how the samples match up. | Note due to a bug in the R script used by the tool this is not produced when only two samples are given.

*.{pdf}

corr_matrix

meta:map

Groovy Map containing sample information about the combined set of files e.g. [ id:'combined' ]

*_corr_matrix.txt:file

A text file containing the correlation matrix between each sample

*corr_matrix.txt

all

meta:map

Groovy Map containing sample information about the combined set of files e.g. [ id:'combined' ]

*_all.txt:file

A txt file containing all the sample comparisons, whether they match or not

*all.txt

matched

meta:map

Groovy Map containing sample information about the combined set of files e.g. [ id:'combined' ]

*_matched.txt:file

A txt file containing only the samples that match with each other

*matched.txt

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
maintainer
Github user sppearce
get in touch
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