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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.
The text was updated successfully, but these errors were encountered:
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.
Hi,
When I genotype known SVs from a VCF, Sniffles2 raise a Fatal error:
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 inSniffles/src/sniffles/vcf.py
). After I manually fill in the QUAL values, Sniffles runs without error.The text was updated successfully, but these errors were encountered: