philippesanio
commented
1 month ago Hi @pcr876
This seems to be caused by the --only-chr chr1,2,5,6,7,9,10,15,17,19,X statement. You did it correctly for chromosome 1 with chr1. However, this has to be the same for the other chromosomes to. Assuming the other chromosomes follow the same naming scheme it should look something like this --only-chr chr1,chr2,chr5,chr6,chr7,chr9,chr10,chr15,chr17,chr19,chrX
I hope this helped! Cheers, Philippe
Hi, I am trying to run spectre for CNV analysis for my targeted cancer data. I am getting the following error. My command line: spectre CNVCaller \ --coverage s101.regions.bed.gz \ --sample-id s101 \ --output-dir spctre_op/ \ --reference GCA_000001405.15_GRCh38_no_alt_analysis_set-002.fasta \ --only-chr chr1,2,5,6,7,9,10,15,17,19,X --cancer --disable-max-coverage --metadata metadata.mdr --blacklist grch38_blacklist_spectre.bed
Error: File "/miniconda3/bin/spectre", line 8, in
sys.exit(main())
File "/miniconda3/lib/python3.9/site-packages/spectre/spectre.py", line 642, in main
spectre_run.spectre_exe()
File "/miniconda3/lib/python3.9/site-packages/spectre/spectre.py", line 356, in spectre_exe
spectre_main.cnv_call()
File "/miniconda3/lib/python3.9/site-packages/spectre/spectreCNV.py", line 88, in cnv_call
self.cnv_analysis.data_normalization()
File "/miniconda3/lib/python3.9/site-packages/spectre/analysis/analysis.py", line 187, in data_normalization
self.coverage = tmp_genome_wide_coverage_dict[reference_chromosome]
KeyError: '2'
Kindly help ! Thank you in advance, Shree