VCF with both SNV and non SNV's

[Takadonet]

I am looking to have both SNV called and non SNV's in the same vcf for downstream analyses.

My temporary workaround at the moment is to run the tool twice, once with the reference to generate the SNV's and other without to get non SNV. Then combine both of them using the SNV vcf's as first pick using vcf-vcf intersect tool

Is this possible?

[karel-brinda]

Hi Phil, I wanted to answer this question and put the answer to the FAQ section in the readme (will be created). However, I realized that I don't completely understand the trick with non-SNVs. Could you explain it in more details, please?

[Takadonet]

Hey Karel,

The overall trick to have both SNV and non-SNV in the same vcf file is to run ococo 2 separate times. First time you run it, you pass the reference file, second time you don't.

After that I combine both vcf output files with vcf-vcf intersect and ensure that SNV only vcf is applied onto of the non-SNV version. Below is part of my Galaxy Workflow.

My hope is to combine aligning, non-SNV calling , SNV calling and vcf vcf intersect into a SINGLE tool/job on Galaxy. Maybe even directly convert it to a bcf file format.

[Takadonet]

@karel-brinda is there any plans to add this feature?