Question: best practices in trio snp and cnv analysis
0
gravatar for mcdm
20 months ago by
mcdm0
Barcelona
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 • 887 views
ADD COMMENTlink written 20 months 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 20 months ago • written 20 months ago by RamRS23k

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

ADD REPLYlink written 20 months 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 20 months ago by RamRS23k

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.

ADD REPLYlink written 20 months ago by Fabio Marroni2.3k
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