Question: Question of INFO parameter (precise) in VCF
0
gravatar for lee.jingu0626
6.1 years ago by
Korea, Republic Of
lee.jingu062630 wrote:

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?

next-gen • 2.2k views
ADD COMMENTlink modified 6.1 years ago by iraun3.8k • written 6.1 years ago by lee.jingu062630
4
gravatar for iraun
6.1 years ago by
iraun3.8k
Norway
iraun3.8k wrote:

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.

ADD COMMENTlink written 6.1 years ago by iraun3.8k
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