CNV kit merge all my gene names together

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3.0 years ago

manojkumarbioinfo ▴ 100

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 • 1.1k views

ADD COMMENT • link updated 3.0 years ago by brunobsouzaa ▴ 840 • written 3.0 years ago by manojkumarbioinfo ▴ 100

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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.

ADD REPLY • link 3.0 years ago by Pierre Lindenbaum 164k

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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.

ADD REPLY • link 3.0 years ago by manojkumarbioinfo ▴ 100

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You can use call function using Tumor.cnr files

ADD REPLY • link 3.0 years ago by brunobsouzaa ▴ 840

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