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
included in
sarek
included modules and subworkflows
bcftools/mpileup ngscheckmate/ncm
maintainer
Github user SPPearce
get in touch
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