--normalize_type creates invalid VCF for translocations

mkirsche / Jasmine

Jasmine: SV Merging Across Samples

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--normalize_type creates invalid VCF for translocations #26

Open wdecoster opened 2 years ago

wdecoster commented 2 years ago

Hi,

I think --normalize_type on a BND representing a translocation creates an invalid VCF, as it fills in the END INFO field with a value that is on a different chromosome, which may end up being END < POS. While that seems, according to the VCF4.2 specifications, not explicitly forbidden, it does lead to errors with bcftools and has been clarified in the VCF4.3 specifications "End position on CHROM ".

See for example also https://github.com/samtools/hts-specs/pull/436

Cheers, Wouter

mkirsche commented 2 years ago

Hi Wouter,

Thanks for bringing this to my attention! I will plan on updating this in the next Jasmine release to conform with these standards.

Thank you!! Melanie

wdecoster commented 2 years ago

Hi Melanie,

That's great. Thank you for the very useful tool. I think this also comes from jasmine, but I think you also added the 'STRANDS' and 'AF' info fields, but these are not yet defined in the VCF header?

Cheers, Wouter