reference letter case issue in VCF

[splaisan]

HI,

sniffles2 VCF results contain sequences in lower case while the reference genome is higher case in that location. This leads to crashing when I phase the VCF using hiphase (https://github.com/PacificBiosciences/HiPhase/issues/19).

Can I fix this issue at the source which seems to be here in future runs?

Thanks for your help

[splaisan]

Hi, Unfortunately, the incompatibility with hiphase does not stop here and also includes the ref and alt notation.

• INS calls give N as ref base instead of the actual first reference base at the insertion point as instructed in the VCF format manifest.
• DEL calls give N as alt sequence instead of the first nucleotide of the deletion as in the manifest. Being able to phase SV calls would be great to have but would require rewriting sniffles2 to comply with VCFV4. Please correct me if I missed something here or if there is a phasing tool that accepts sniffles2 data as input Thanks for the otherwise great tool Stephane