Birdsuite: output files

Question

[Taylor95]

Dear all,

I'm trying to use Birdsuite for CNV analysis and confused about its output files. Which one I can use? In the Output-files section(https://www.broadinstitute.org/birdsuite/output-files), it explains that BASE.birdseye_canary_calls is merged Birdseye and Canary calls, BASE.canary_calls is calls file for common CNPs and BASE.birdseye_calls is raw Birdseye calls. In the Overview section(https://www.broadinstitute.org/birdsuite/birdsuite-overview), it says Canary genotypes common copy-number polymorphisms (CNPs) and Birdseye detects Rare/de novo copy-number variants (CNVs). So, are CNVs all common CNPs or rare CNVs that remove common CNPs in BASE.birdseye_canary_calls? If they are all common CNPs, aren't the calls all rare in BASE.birdseye_calls?

Thanks in advance!

Answer 1

[Kevin Blighe]

Copy number variant / copy number variation (CNV) is a general term that has a different meaning to different people. In this context, I would regard CNV as encompassing both 'rare CNV' and 'common CNV', with 'common CNV' also being regarded as CNP (copy number polymorphism).

In the same way, we would distinguish 'rare variant' from single nucleotide polymorphism (SNP), even though rare variants are still SNPs.

In terms of which output file to use, that is not for us to tell you. That is for you to tell yourself. You have already outlined the contents of each file in your question; so, now choose which one you need.

Kevin