Golden set document

[OrsonMM]

Dear team MBaysanLab,

Please, can you explain "Golden set" VCF.

In my case, I have 8 samples.

3 of Raze A and 5 of Raze B.

Using bcftools isec, I obtained SNPs merge of Raze A and B.
using VCF-observer I am tryng to make a Venn plot.

But in "Compare set" I am attach the Raze_A.vcf and Raze_B.vcf.
I am not understand that file for "Golden set",

Please, any support.

[asimemul]

Hello,

The golden set is a VCF file containing known true variants. It is used when calculating precision and recall values for the "precision-recall plot".

However, it is not used for the Venn diagram.

Did you have any problems when creating the Venn diagram?

[OrsonMM]

Hi,

Yes, it works well, creating the Venn diagram .

another question.

What file of GENBANK is accepted for .BED ?

Or you recommend a format more simple ?

Thanks .

[asimemul]

Yes, currently only simple BED format is supported.

Is it possible for you to share your use case?