Add support for VCF inputs for SV Matrix Generation

[mdbarnesUCSD]

• Add support for VCF inputs for SV matrix generation
• Update README

[DarioS]

Particularly VCF version 4.4, which has enhancements for structural variant representation and deprecates the SVTYPE field.

[MousumyCSE]

Hi DarioS,

Thank you for letting us know!

If you could share any example files for the structural variant VCF 4.4 version with us, that would be amazing. That way, we could update our workflow as well.

Best, Mousumy

[DarioS]

Yes, please see COLO829v003T.purple.sv.vcf example file and ignore ##fileformat=VCFv4.2 in the header section.

GRIDSS uses HTSJDK which writes VCF version 4.2. So, yes, that technically makes it non-compliant with version 4.4. That said, the content of the actual records are compliant with the version 4.4 specification.

Source: Daniel Cameron, GRIDSS creator.

[MousumyCSE]

Hi @DarioS,

Thank you for sharing! We will be working on this.

Best, Mousumy

[DarioS]

Is it ready to run yet?

[mdbarnesUCSD]

We moved forward with support for inputs for SV VCFs versions 4.1, 4.2, and 4.3. In a future release we hope to add support for VCF versions 4.4 and 4.5.