Philippe Sanio

Hi @pcr876 Thanks for reaching out. The output of the images should just give you an idea where the CNVs are located and how the signal performs. It sould look...

Hi @leahkemp Thank you for raising this question! For XX samples, you do not need to specify the ploidy state of chrY, because Spectre is using the blacklist that excludes...

Hi @gsneha26 Thank you for your very detailed issue description. I will take a look and get back to you ASAP! Best, Philippe

Hi @gsneha26 Looking at the data and Spectre's code, chromosome M produces an error because Spectre is restricted to a minimum chromosome length of 1 MB. Thus, small chromosomes like...

Hi @gsneha26 I just added the flag `--min-chr-len` that should overwrite the default value of the minimum chromosome length. You can just add it to your Spectre command, e.g. `--min-chr-len...

Hi @fidibidi Thanks for pointing this out! This is in fact not a bug. **Spectre is designed to detect large CNVs >= 100kb**. Below 100kb the chance of FPs will...

Hi @zaka-edd My applogies for the late reply. Two things are happening here: > Coordinate

Hi @reshu23 The 6th column of the BED file is the median coverage of the CNV. If it is 0.0 it would be DEL with a copy number of 0...

Hi @Schmytzi Thank you for pointing this out! Yes, we definitely have publishing Spectre on Bioconda on our roadmap and are planning to do this with the next release. I...

Hi @reshu23 My apologies for the late reply. > Should I assume that, Spectre wont report exact breakpoint? Yes, Spectre will not report the exact breakpoint. The reported start and...