Open fidibidi opened 1 month ago
Hello @fidibidi,
Thank you for raising this issue. The warnings you're seeing are likely due to the small chromosome sizes, such as chrM and unplaced contigs, where the number of positions to be tested is very limited. These warnings generally do not significantly affect the results and can be safely ignored in this context.
Regarding the use of --min-cnv-len
set to 10kb, we do not recommend this configuration as it can lead to an increased number of false positives (FPs). For events smaller than 100kb, we suggest using Sniffles, which is more suited for handling such cases.
Please let us know if you have any further questions or concerns.
Best Regards, Alexey
Ran on sample using command:
Spectre ran, but produced this worrisome message during its run.
In the end, a vcf was generate with no found CNVs. However, when a command (similar but modified with vanilla spectre in mind) is run, the vcf contains CNVs.