What are the best tools/practices for CNV (structural variation) detection/analysis for Illumina family data?

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6.9 years ago

Irina Astrovskaya ▴ 20

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 sv snp array wes wgs • 2.5k views

ADD COMMENT • link updated 5.3 years ago by h.mon 35k • written 6.9 years ago by Irina Astrovskaya ▴ 20

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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 REPLY • link 5.3 years ago by Ram 43k

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