Copy number variation from BAM and VCF files?

Question

[dog.seal6363]

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

[Sean Davis]

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

Answer 1

[Chirag Nepal]

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.

[dog.seal6363]

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

[Chirag Nepal]

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