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Add somalier to identify sample swaps

Open grst opened this issue 5 months ago • 3 comments

Description of feature

We recently found somalier quite useful to uncover sample swaps etc. Could be nice to include this by default.

Output: relatedness matrix. To be included as heatmap in multiqc report.

CC @apeltzer

grst avatar Jul 31 '25 08:07 grst

Would be good to have the *groups.tsv also shared in the outputs so that one can investigate

apeltzer avatar Jul 31 '25 08:07 apeltzer

Hmm, maybe trickier: Needs several assumptions around data, e.g. organism type, sites files and mapped files.

apeltzer avatar Aug 07 '25 13:08 apeltzer

Yeah, I think you'd want to include a tool that works on fastq files, not bam files. ntsm is an option that is more recent than ngscheckmate and may be more maintained.

SPPearce avatar Sep 01 '25 09:09 SPPearce