Unable to open VCF produced by OctopuSV using BCFTOOLS

[JoannaTan]

Hi,

Thank you for the great too.

I am trying to merge SVs across different tools. however, After the merging, i am unable to open the file using bcftools.

Failed to read from octopusMerged.vcf: unknown file type

Is this expected?

Thank you.

Best regards,
Joanna

[qingxiangguo]

Hi Joanna,

First, really thanks for using this tool. We're actively collecting all the issues and expect to incorporate them in the next version.

Could you upload your octopusMerged.vcf (or a subset), so I can check what happened?

[JoannaTan]

I think i found the issue with the VCF. The first line of the VCF fileformat should be VCF instead of SVCF?

##fileformat=SVCFv1.0
##fileDate=2025-06-02|07:46:09AM|
##source=octopusV
##contig=<ID=chr1,length=248956422>

[qingxiangguo]

I think i found the issue with the VCF. The first line of the VCF fileformat should be VCF instead of SVCF?

##fileformat=SVCFv1.0
##fileDate=2025-06-02|07:46:09AM|
##source=octopusV
##contig=<ID=chr1,length=248956422>

Yes, I think it's the reason. We'll revise this in the update.