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

Description

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

name

description

pattern

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

BAM files for each sample

*.{bam}

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

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

*.{bed}

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

fasta file for the genome

*.{fasta}

name

description

pattern

A pdf containing a dendrogram showing how the samples match up

*.{pdf}

A text file containing the correlation matrix between each sample

*corr_matrix.txt

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

*matched.txt

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

*all.txt

vcf files for each sample giving the SNP calls

*.vcf

File containing software versions

versions.yml