Hello, While I'm aware its not the best tool for detecting relatively small CNVs, I'm trying to use CNVKit to detect a single exon deletions. I have a very small panel of genes (~10) with very high coverage (>1000). However when I run
cnvkit.py coverage sample123.bam one_row.bed -o sample123.cnn
where one_row.bed has a single regions spanning few bases (I tried 200 bases and 5 bases). I'm looking at the bam file and each base in this region has >1000 depth, but still, the depth in the cnn output file is very low (~10).
What am I missing? Shouldn't the depth hold the average depth of all the bases in the region?
Thank you for the help.