Question: Linkage with WES data using Merlin
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gravatar for Maverick77
4 months ago by
Maverick770
London
Maverick770 wrote:

Hi there,

I would like to perform linkage analysis with whole exome data from 7 families = 36 individuals each with a vcf file.

I have completed the merlin installation and associated tutorial. I want to complete a parametric analysis using a dominant inheritance model.

https://csg.sph.umich.edu/abecasis/Merlin/tour/parametric.html

Merlin was recommended but I am happy to use other software it is more straightforward.

My question involves the construction of the .map file and data file.

  1. How do I create a map file or a file with uniform markers obtained from the vcf files from each individual?

  2. Are markers obtained from a reference genome file and annotated to the vcfs?

If you have done this kind of analysis before a step-by-step process of how you conducted the analysis including any file conversions to plink etc would be greatly appreciated.

exome data merlin linkage • 199 views
ADD COMMENTlink written 4 months ago by Maverick770
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