Question: Copy number variation from BAM and VCF files?
0
gravatar for dog.seal6363
3.4 years ago by
United States
dog.seal63630 wrote:

Hello,

I was wondering if anyone knows how I could determine the copy number variation data from BAM and/or VCF files. I only have these two file formats, but I would really like to know if I could determine whether there is homozygous deletion or other types of deletions from these files. Or, if there is any other way I could determine homozygous deletions, that would be very helpful too. 

Thanks. 

cnv bam vcf • 2.3k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by dog.seal63630
1

Exome or genome data?  Tumor?  Associated normal?  How many samples?

ADD REPLYlink written 3.4 years ago by Sean Davis25k
0
gravatar for Chirag Nepal
3.4 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

I had posted a tutorial on how to analyze exome CNV. Have a look, if it can be of any help.

Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.

 

 

ADD COMMENTlink written 3.4 years ago by Chirag Nepal2.2k

Thanks, but it doesn't mention anything about BAM or VCF files. It's all tumor data.

ADD REPLYlink written 3.4 years ago by dog.seal63630

From your Tumor/Normal bam pair, create mpileup from samtools, then input that mpileup file to varscan copycaller as described in tutorial.

ADD REPLYlink written 3.4 years ago by Chirag Nepal2.2k
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