Open pcr876 opened 4 days ago
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 something like this:
The pink lines describe the DEL/DUP thresholds, and the black line is the normalized coverage mean * ploidy state of the chromosome.
Based on our output images (chr7 and chr9) it seems there is something off.
Questions:
When running Spectre in the cancer mode, we highly recommend you using SNV data in the form of a VCF, which can be provided with the --snv
. Spectre then calculates the copy number neutral state from the SNV data instead of the coverage. We did that since cancer samples can be highly mutative, which would result in enormous coverage ranges in the genome.
Best, Philippe
please see my question about SNV files with cancer/tumour data #34 . Thanks in advance
Hi I have know cnvs. I am running spectre for my targeted sequenced data for cancer. I am not getting the output what I expected to see. Also I have trouble understanding the images. Following is the command I used:
spectre CNVCaller \ --coverage spectre/mosd.regions.bed.gz \ --blacklist grch38_blacklist_spectre.bed \ --metadata spectre/metadata.mdr \ --sample-id spectre_101 \ --only-chr chr1,chr2,chr5,chr6,chr7,chr9,chr10,chr15,chr17,chr19,chrX \ --cancer \ --disable-max-coverage \ --output-dir spectre/ \ --reference reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
Also I have attached the images I have obtained running spectre:
Thank you in advance,
Shreya