Dear all, I'm usign cnvkit in a germline-mode (no tumors).
I set the threshold in "cnvkit call" and I can see several regions with different cn number in the output.
Moreover I tried to used the genemetrics command in order to obtain the list of genes with CNV.
If I well understood, with "call" I have the output based on big regions (not genes-specific), while genemetrics is focused only on genes.
I have some questions:
why not all the CNV with cn different form 2 in the call output, are listed in the txt (genemetrics)?
why I have big region with cn=2 in the call file, but I can see one gene included in this region with cn=3 in the genemetrics file? I am supposed to see comparable results.
Morover, I used the scatter plot in order to have a representation of the chromosome region with the CNV. This is the command: cnvkit.py scatter sample.call.cnr -s sample.call.cns --segment-color red -c chr5 -g genename --y-min -2 --y-max 2.5 -o nomeoutput.png (cnvkit version 0.9.9)
The image is compound only with red dots with no light grey dots (as reference) as I saw in the web. Can you help me?
Dear all, I'm usign cnvkit in a germline-mode (no tumors). I set the threshold in "cnvkit call" and I can see several regions with different cn number in the output. Moreover I tried to used the genemetrics command in order to obtain the list of genes with CNV. If I well understood, with "call" I have the output based on big regions (not genes-specific), while genemetrics is focused only on genes. I have some questions:
Morover, I used the scatter plot in order to have a representation of the chromosome region with the CNV. This is the command: cnvkit.py scatter sample.call.cnr -s sample.call.cns --segment-color red -c chr5 -g genename --y-min -2 --y-max 2.5 -o nomeoutput.png (cnvkit version 0.9.9) The image is compound only with red dots with no light grey dots (as reference) as I saw in the web. Can you help me?
thank you in advance