hey so urgent bug I found... I don't really understand why nobody noticed this. essentially manta runs on all samples in the sample sheet but with a randomness due to the channel input. all the other tools seems to run one-by-one on each sample. so a second bug in svdbmerge where it doesn't check the sample names in the vcf essentially replaces all the merged vcf samples with the sample names of the first priority vcf. if you were running WGS manta doesn't take precedence so you would just get FP from manta. for me with WES, manta takes precedence so I'm getting potential FN from ALL other tools (include my main cnv powerhouse gatk germlinecnv caller). which given the way we are supposed to be analysing sample in accordance with Swiss regulations would result in critical cnvs being missed !!!! hopefully everyone is running this pipeline on 1 patient at a time per sample sheet or on trios as this would mostly avoid problems... but scary nonetheless https://github.com/nf-core/raredisease/issues/814