Add VCF support to the predict command

[nvnieuwk]

A new argument --vcf should be created which will create the output in VCF format.

[nvnieuwk]

I will probably follow the format stated here: https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/CNVVCFFile_fDG_dtSW.htm

[nvnieuwk]

VCF format v4.3: https://samtools.github.io/hts-specs/VCFv4.3.pdf

[Bio-finder]

Hello,
I would be interested in this feature. Do you plan to implement it soon or should I find a way to convert my bed files. If I need to convert them, do you have a tool that you would recommend to convert wisecondorx bed to vcf?
Best regards,

[matthdsm]

We don't really have much time for new developments right now. It should be added in the future.

In the mean time you can use https://github.com/nvnieuwk/bedgovcf

[Bio-finder]

Ok thank you.

[nvnieuwk]

You can find a config I use for WisecondorX specific output in Bedgovcf here: https://github.com/nf-cmgg/structural/blob/master/assets/bedgovcf/wisecondorx.yaml