Dear all,

does anybody have experiences with this examle in variant calling:

Lets assume reference is:

AAA**CGT**AAA

And its aligned reads is:

AAA**GGC**AAA

My output from VarScan is:

4C>G
6T>C

But some algorithms detected variants like:

delCGTinsGGC

Finally this indels seems to be describe in databases and valid. Does anybody can tell, if some variant caller can report indels at once? And what is biologically valid?

Please this is only demonstration. I can add real data.

Paul.