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

Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data

Other

121 stars 20 forks source link

somatic l can be run either with or without a matched normal control sample ? #101

Open worker000000 opened 5 years ago

worker000000 commented 5 years ago

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 commented 5 years ago

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

worker000000 commented 5 years ago

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

worker000000 commented 5 years ago

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

eroller commented 5 years ago

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.