pos of interspersed duplication

[bakeronit]

Hi all,

got confused by the vcf annotation of duplication. The annotation of DUP:INT includes the start pos, end pos and SVLEN. I found that end-start is always equal to SVLEN. So I guess the start and the end coordinates describe the start and end of the original segment been duplicated.

I am wondering where is the relative reference coordinate of the new duplicated sequences? if it's not tandem dup.

Cheers Jia

[jamesdalg]

That would be really helpful. I looked at one of these and as it stands now, it creates a CN peak in the of duplicated region and the VCF will state if it is a cut and paste duplication, but the VCF does not report where the duplication was actually inserted. If you can, please include this information in the next version. You can choose either piece of information with the interspersed duplications as insertions flag.