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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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Fatal error when genotyping VCF with missing QUAL #506

Closed Han-Cao closed 2 weeks ago

Han-Cao commented 3 months ago

Hi,

When I genotype known SVs from a VCF, Sniffles2 raise a Fatal error:

Sniffles2 Error: Error parsing input VCF: Line 211: invalid literal for int() with base 10: '.' (Fatal error, exiting.)

It seems this is due to the QUAL in my VCF is ".". It cannot be parsed by the read_svs_iter method as an integer is expected (line 315 in Sniffles/src/sniffles/vcf.py). After I manually fill in the QUAL values, Sniffles runs without error.

hermannromanek commented 3 months ago

Hi Han-Cao,

Thanks for the report and the analysis - this is indeed an error, according to the VCF spec '.' is an allowed value for qual. I'll fix it for the next release of sniffles.

Thanks, Hermann

hermannromanek commented 2 weeks ago

Fixed for 2.5