Question: best practices in trio snp and cnv analysis
gravatar for mcdm
2.9 years ago by
mcdm0 wrote:

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.

omni5 cnv snp gwas trio • 1.3k views
ADD COMMENTlink written 2.9 years ago by mcdm0

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

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by RamRS30k

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

ADD REPLYlink written 2.9 years ago by mcdm0

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.

ADD REPLYlink written 2.9 years ago by RamRS30k

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:

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.

ADD REPLYlink written 2.9 years ago by Fabio Marroni2.6k
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