Question: Cnv Analysis Of Complete Genomic Data
4
gravatar for rob.costa1234
6.4 years ago by
rob.costa1234240
United States
rob.costa1234240 wrote:

I am looking for a suggestion how to analyze CNV data from CG. There are two type of files of CNV data - somatic CNV segmentation and second is depth of Coverage. I would like to see CNV among tumor vs normal samples.

Thanks.

cnv genomics • 2.7k views
ADD COMMENTlink modified 10 months ago by bioinformatica0 • written 6.4 years ago by rob.costa1234240

I have a little problem with CNVkit.

I normally use cnvkit to calculate CNV in a whole exome panel and I have no problems and I have a good results. But now I'm trying to calculate them in a smaller panel (50 genes). The commands Ihave used are the same but with a different bed file.

cnvkit.py batch sample_sorted_ND.bam --normal *sorted_ND.bam -t my-targets.bed --fasta hg19_ref_genome.fa --access data/access-5kb-mappable.hg19.bed --output-reference my_Mreference.cnn --output-dir example1

The problem is that, when I look at the log2 in the cnr file, the only regions I have out of range are BRCA1_14 and BRCA_13, which is the deletion that there really is.

chr17 41228504 41228631 427_15619_672(BRCA1)_14 142535 -0.540179 0.629573 chr17 41231350 41231416 427_15618_672(BRCA1)_13 119045 -0.672668 0.552469

But in the diagram comes out many genes (most of the genes in the panel but not BRCA1), Why? Should not only go uot these regions? I am doing something wrong? I must add something else on the command line?

Other question is that the deph column is not correct since it does not always recognize decimals.

Some one can help me?

Thank you,

Kira

ADD REPLYlink written 10 months ago by bioinformatica0

Please create a new thread with you question. It is not a good idea to post new question in existing threads. Then come back and delete this post.

ADD REPLYlink written 10 months ago by genomax83k

Sorry,

I try to open a new post and I don't know why now is here.

Kira

ADD REPLYlink written 10 months ago by bioinformatica0

Use New Post button at top right of main page.

ADD REPLYlink written 10 months ago by genomax83k
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