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

description

pattern

`ch_input`

BAM/CRAM file for each sample.

Structure: [ val(meta1), path(bam) ]

*.{bam,cram}

`ch_snp_bed`

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

Structure: [ val(meta2), path(snp_bed) ]

*.bed

`ch_fasta`

Fasta file for the genome and its index.

Structure: [ val(meta3), path(fasta), path(fai) ]

Output

name

description

pattern

`corr_matrix`

A text file containing the correlation matrix between each sample.

Structure: [ val(meta), path(corr_matrix) ]

*corr_matrix.txt

`matched`

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

Structure: [ val(meta), path(matched) ]

*matched.txt

`all`

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

Structure: [ val(meta), path(all) ]

*all.txt

`vcf`

vcf file for each sample giving the SNP calls.

Structure: [ val(meta), path(vcf) ]

*.vcf.gz

`pdf`

A pdf containing a dendrogram showing how the samples match up.

Structure: [ val(meta), path(pdf) ]

*.pdf