Question of INFO parameter (precise) in VCF

Question

[lee.jingu0626]

Hi.

I have a question about VCF file type.

After I performed structural variation detection tool, I got output file of VCF.

In VCF, column of INFO had variable named 'precise' and 'imprecise'.

VCF file type provided by 1000genome so I get some information about 'precise' and 'imprecise'.

But I confuse about difference between these two types.

How can I separate these two types?

Answer 1

[iraun]

In the VCF specifications you can read that...:

##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">

If you see the FORMAT column, you can see DR (high-quality reference pairs) and DV (high-quality variant pairs) variables. DR & DV represent counts for reference and SV supporting paired-ends, which are then fed into the genotyping model to derive genotype likelihoods, a genotype quality and the final genotype call. For precise events (INFO:PRECISE), Delly uses RR & RV, which are the reference and SV allele supporting reads (not pairs) because the exact breakpoint sequence is known.

Hope it helps.