CNV detection tools for NIST samples

Question

[LimMo]

Hello all,

I'm interested in finding CNVs, the problem is that I follow a number of papers (CNV kit, Breakdancer, LUMPY and PennCNV) on the public sample from NIST (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x)

The problem is none of these tools captures that much (very few).

And I'm comparing that to NIST gold standard (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NA12878_PacBio_MtSinai/)

So, are there other best tools that could tackle this problem or help me to do that?

Thanks.

Answer 1

[Kevin Blighe]

There are countless CNV callers in bioinformatics and, as with everything else in this field, disagreement is high among these programs. Keep in mind, though, that the NIST reference samples themselves are flawed and have not been screened by gold standard technology(ies).

For CNV, your best bet is to find the consensus calls among multiple programs. However, the only program that I use these days (for calling copy number variants / alterations from NGS data) is Control-FREEC. For microarrays, I'd use Aroma Affymetric (for Affymetrix microarrays).

Kevin