Minimum CNV length must be greater then 10000 base pairs

[fidibidi]

Running command with --min-len-cnv 10000; gave me the following error.

spectre::2024-09-30 22:53:53,318::ERROR::spectre.analysis.analysis> Minimum CNV length must be greater then 10000 base pairs

However when run with the --min-len-cnv set to 11000... it worked

  spectre CNVCaller \
  --dist-proportion 0.3 \
  --coverage input-files/A0035.regions.bed.gz \
  --sample-id A0035 \
  --output-dir A0035_spectre_output/ \
  --reference ~/refs/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
  --blacklist data/grch38_blacklist_0.3.bed \
  --min-cnv-len 11000 \ //when set to 10000 i get the error
  --snfj input-files/A0035.wf_sv.snfj.gz \
  --snv input-files/A0035.wf_snp.vcf.gz \
  --metadata data/grch38_metadata.mdr

``

Seems like a bug maybe? 

[philippesanio]

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 dramatically increase the further below you go under min-cnv-len of 100kb (depending on the signal-to-noise ratio of your sample)

spectre::2024-09-30 22:53:53,318::ERROR::spectre.analysis.analysis> Minimum CNV length must be greater then 10000 base pairs

This message is shown, because Spectre uses at least 10kb to deal with noise in the data.

Best, Philippe