CNV kit merge all my gene names together

Hi, I'm using cnv kit for my copy number variant analysis, I'm facing some issues whenever I call CNV my gene names are combined together for example as shown in the image below

does anyone know to fix this issue? I'm using target sequencing

command used

python cnvkit.py batch my.bam --targets my_targets.bed -n --fasta hg38.fa --output-dir test_run --diagram --scatter --diagram --annotate refFlat.txt --access access-10kb.m10.bed

enter image description here

cnv cnvkit

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updated 4.6 years ago by brunobsouzaa

• written 4.6 years ago by manojkumarbioinfo

gene names are combined together *

I don't get your problem. If you have a CNV in "chr3:72230415-91426092", you'll overlap 3 genes: RYBP, SHQ1, EPHA3.

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written 4.6 years ago by Pierre Lindenbaum

I don't want the gene name and location to be combined. I want to be separate for example RYBP chromosome start - end its log-ratio.

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written 4.6 years ago by manojkumarbioinfo

You can use call function using Tumor.cnr files

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written 4.6 years ago by brunobsouzaa

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