Question: What are the best tools/practices for CNV (structural variation) detection/analysis for Illumina family data?
1
gravatar for Irina Astrovskaya
2.0 years ago by
USA/ NYC
Irina Astrovskaya20 wrote:

Hi,

I am looking for the current state-of-the-art tools/practices for CNV (structural variation) detection/analysis for family (trio) data produced by Illumina.

I will have data obtained on Illumina SNP arrays as well as from Illumina whole exome sequencing and whole-genome sequencing.

What would be the best tools to apply for each technology? Any advice/suggestion is highly appreciated:)

Thank you!

cnv wes snp array wgs sv • 1.2k views
ADD COMMENTlink modified 6 months ago by h.mon26k • written 2.0 years ago by Irina Astrovskaya20

We used XHMM for Whole Exome data. There is a step-by-step guide to get to CNV calls from BAM files here. Also, plink/seq has a cnv-denovo utility (I think that's what it's called) to detect de novo and transmitted CNVs. This paper should be useful.

ADD REPLYlink written 6 months ago by RamRS22k
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