Description

Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’]

files:file

VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too.

*.{vcf,vcf.gz,bam,bai}

meta2:map

Groovy Map containing SNP information e.g. [ id:‘test’ ]

snp_bed:file

BED file containing the SNPs to analyse

*.{bed}

meta3:map

Groovy Map containing reference fasta index information e.g. [ id:‘test’ ]

fasta:file

fasta file for the genome, only used in the bam mode

*.{bed}

Output

name:type
description
pattern

corr_matrix

meta:file

A text file containing the correlation matrix between each sample

*corr_matrix.txt

*_corr_matrix.txt:file

A text file containing the correlation matrix between each sample

*corr_matrix.txt

matched

meta:file

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

*matched.txt

*_matched.txt:file

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

*matched.txt

all

meta:file

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

*all.txt

*_all.txt:file

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

*all.txt

pdf

meta:file

A pdf containing a dendrogram showing how the samples match up

*.{pdf}

*.pdf:file

A pdf containing a dendrogram showing how the samples match up

*.{pdf}

vcf

meta:file

If ran in bam mode, vcf files for each sample giving the SNP calls used

*.vcf

*.vcf:file

If ran in bam mode, vcf files for each sample giving the SNP calls used

*.vcf

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
included in
sarek
maintainer
Github user sppearce
get in touch
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