LUMPY SV call without quality score

Question

[bxia]

I am using LUMPY to call structure variation, but the problem is all the quality score returned by LUMPY is marked as '.'

Is it due to low sequencing depth?

[Pierre Lindenbaum]

or may be there is just no QUAL... why would it be a "problem" ?

[bxia]

I checked the other people's post, they have it and all the REF column are shown as N..

[Pierre Lindenbaum]

I've got some lump-sv (lumpy express) in my server: there is no QUAL.

[bxia]

But the other problem I have is the REF column are all N, although it tells me it is DEL or INDEL or something else..

[Pierre Lindenbaum]

again, why do you need this information. Imagine you have a deletion of 1 megabase; unless you're using a symbolic allele, it would need a VCF file with a REF allele of 1E6 characters....

[bxia]

Thanks for your explanation. I have read the VCF format description, I thought it will tell me the details of the changes..