VCFv4.4 is not a supported version

[eroller]

Hi, I tried to load a VCF file that uses VCF 4.4 which is the latest specification:

https://github.com/samtools/hts-specs/blob/master/VCFv4.4.pdf

and got an error:

Error loading ....vcf.gz. Unable to parse header with error: Your input file has a malformed header: VCFv4.4 is not a supported version for input source: ....vcf.gz

Generally the vcf spec seems to be forward compatible so I was wondering what is the need for rejecting future versions of the VCF specification? Can we safely remove this error without major changes to IGV?

[jrobinso]

That's a question for the htsjdk, @lbergelson ?

[lbergelson]

Unfortunately htsjdk doesn't support 4.4 yet. There are some changes in 4.4 that are not compatible with previous versions ( leading | in GT field and genotype number value P for instance. ). In many cases they will be compatible but you might run into issues. There's no current plan/timeline to support 4.4 although it's an obvious thing that people want. Adding an option to disable version validation and just give it a shot seems plausible as a stopgap measure.

[droazen]

@KevinCLydon will add the capability to toggle VCF version validation as a stopgap measure until full 4.4 support is implemented in HTSJDK.