bam_ngscheckmate

Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.

ngscheckmateqcbamsnp

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_ngscheckmate

Description

Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs.

Input

name:type

description

pattern

`meta1 :map`

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

`bam :file`

BAM files for each sample

*.{bam}

`meta2 :map`

Groovy Map containing bed file information
e.g. [ id:‘sarscov2’ ]

`snp_bed :file`

BED file containing the SNPs to analyse. NGSCheckMate provides some default ones for hg19/hg38.

*.{bed}

`meta3 :map`

Groovy Map containing reference genome meta information
e.g. [ id:‘sarscov2’ ]

`fasta :file`

fasta file for the genome

*.{fasta}

Output

name:type

description

pattern

`pdf :file`

A pdf containing a dendrogram showing how the samples match up

*.{pdf}

`corr_matrix :file`

A text file containing the correlation matrix between each sample

*corr_matrix.txt

`matched :file`

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

*matched.txt

`all :file`

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

*all.txt

`vcf :file`

vcf files for each sample giving the SNP calls

*.vcf

`versions :file`

File containing software versions

versions.yml