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tjiangHIT / cuteSV

Long read based human genomic structural variation detection with cuteSV
MIT License
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trio analysis recommendation #75

Open prasundutta87 opened 2 years ago

prasundutta87 commented 2 years ago

Hi,

I will be performing trio analysis for SVs. Is there any recommendation for trio analysis using cuteSV (joint genotyping or any tested workflow)? I will be using minimap2 as an aligner.

Regards, Prasun

tjiangHIT commented 2 years ago

Hello @prasundutta87,

Do you mean you want to obtain the SV calls for the child with the aid of the parental samples？ If so, you can refer to the Mendelian inheritance laws to post-filter the zygotic discordant variants. And could you please provide more details about the trio analysis if I misunderstand?

Best regards, Tao

prasundutta87 commented 2 years ago

Hi Tao,

Thanks for the reply. I have sequences for all three samples: father, mother and child and my intension is to filter variants based on mendellian inheritence, like the example you specified. Like for example using bcftools +mendelian?

Regards, Prasun