best practices in trio snp and cnv analysis

Question

[mcdm]

Hi all,

I have Illumina omni5 array data for a family affected by a different grade neurological disorder. I performed snp and cnv calling for each family member with Genome Studio and now I would like to discover specific events causing the different disorder grade in the affected individuals. Do you know any best practices paper or bioinformatic protocol for this kind of analysis, the QC performed and the software used?

Thanks in advance.

[Ram]

My team uses PLINK/SEQ - it has denovo and cnv-denovo sub-programs that help you discover de novo and transmitted variants.

[mcdm]

Thanks I though it was only used for NGS data. I will ckeck it.

[Ram]

You're correct, it's only for NGS data, AFAIK. I'm sorry - I did not (and still do not) know what an omni5 array was.

[Fabio Marroni]

Bu maybe you can use plink. I suggest you give a look at the old manual page and then refer to the new page for downloading and having updated info. Also there are pipelines out: https://redmine.igm.cumc.columbia.edu/projects/biopipeline/wiki/Trio-Analysis_Pipeline

Probably the pipeline itself was conceived for NGS, bout once you obtain your genotype in vcf format you have the same data structure than an NGS experiment.