Detecting loss of heterozygosity (LoH) regions and creating plots

[olya2808]

Hello!
Previous version of ont-spectre (v0.2.1-alpha) stated that it can use SNV data to detect loss of heterozygosity (LoH) regions does it still apply to current (v0.2.2) version? If so, are there arguments that allow this option while launching spectre?

And another question: the previous version of ont-spectre created plots additionaly to bed, vcf, etc. files, does this version create any plots? Are there arguments to turn this option on? When i launch ont-spectre only with required arguments, it doesn't create any plots.

[oxygen311]

Hi @olya2808

Thank you for raising this issue. To clarify, the versions of ont-spectre fork are different from those of the original Spectre. Current ont-spectre fork is based on Spectre v0.2.0 – we’ve just updated the README to reflect this more clearly.

Regarding your questions:

1. Loss of Heterozygosity (LoH): The current version of ont-spectre (v0.3.2) does not support LoH detection because it was not part of the Spectre v0.2.0 version from which it’s based on. If you are interested in LoH detection, we would recommend using the original Spectre v0.2.1-alpha release. We plan to integrate LoH feature to the ont-spectre fork after additional testing.
2. Plots Generation: Plots generation was removed from ont-spectre starting with v0.2.2 (link to changelog). If the plots are required, the original Spectre v0.2.1-alpha release can provide this functionality.

Sorry for inconvenience and please let us know if you have any further questions or concerns.