18 months ago by
I'm guessing you're after germline CNV callers since you've mentioned CNVnator. I've included some suggestions below for read-depth based callers including ExomeDepth which is the one I've used the most (reasonably easy to use since it's an R package). I'd have a look at Ximmer if you're interested in comparing CNV callers since it provides a standardised framework for comparing callers out of the box.
I guess you could try Read-depth callers, callers that look for breakpoints, or split-read (although these are more for WGS than targeted / Exomes), callers that look for missing / moved mate-pairs, or read-pair. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394692/
There's also assembly based callers and callers that use a combination of the above techniques.
The approach you use will also depend on the library and the size of CNV you're looking for.
Generally I've only compared CNV callers after a pipeline that uses BWA for alignment and then GATK best practices, since a couple of the callers actually use parts of the GATK suite (like XHMM). Some CNV callers like CANVAS (https://github.com/Illumina/canvas) are optimised for their own workflow (in this case ISAAC).
Read-Depth based callers
XHMM used by ExAC to call their CNVs
Framework for running mulitple CNV callers together and calculating sensitivity etc. Comes with ExomeDepth, Xhmm, Cnmops and Conifer
GATK4 germline CNV caller https://software.broadinstitute.org/gatk/best-practices/workflow?id=11148
Not sure if this is available yet but should be ready soon - ideal if you want a full GATK best practice pipeline
Mainly used ExomeDepth on Targeted panels and found it okay with some tweaks and heavy filtering for false positives.
modified 18 months ago
18 months ago by
Garan • 580