REF allele is N for all SV types

[weilu1998]

Hi,

I used Sniffles2 to generate a VCF file from 3 samples with ONT reads. When I look at the REF allele column, I found that they are all represented by N. I am wondering is there a particular reason for that? I am planning to used the VCF for other short-reads based genotyping software and the Ns in REF column will cause a lot of trouble.

Thanks, Wei

[yangxin-9]

I have the same problem have you solved it yet?

[fritzsedlazeck]

Hi, so the N as the reference allele is a valid option. We are planing to fill out the reference sequence at some point of our development, but nothing is planed to do that in the next few weeks.

Thanks Fritz

[yangxin-9]

Thanks so much for response.