somatic l can be run either with or without a matched normal control sample ?

[worker000000]

In the paper, it said the latter workflow, I guess not pointing somatic, am I right, thanks a lot.
https://academic.oup.com/bioinformatics/article/32/15/2375/1743834

[eroller]

Correct, referring to workflow for analyzing exome sequencing data (i.e. Somatic-Enrichment)

[worker000000]

but how it ensure the result is right, without the control. thanks a lot

[worker000000]

because most tools need PoN or paired, thanks a lot.

[eroller]

CNV calling on enrichment data should have a paired normal or PoN due to variability in coverage between targets. The sentence here is mainly to point out that the enrichment mode has the additional capability of running with control samples, which isn't an option for the other workflow. The quality of CNV calls on enrichment data will suffer without control samples.