I have exome sequencing and whole genome genotyping data of samples from a family with complex disease. I have performed linkage analysis using merlin. What is the best way to utilize both the data? I have checked that variants with LOD > 1.5 are not in LD with the variants that segregated with only affected members from the family (using exome sequencing data). Is there any other way to use the linkage data for strengthening with the findings of exome data? Am I missing something?
You are missing full-genome data. Only then can you be sure you've found the variants responsible for the disease.
Hi Jan.. Yes I know I don't have the whole genome sequence data.. but I just want to know if there's a way to strengthen my exome data with the findings from linkage analysis?
use exome sequencing alone, can be very powerful tool to find common and rare genetic variants for complex diesease like cancer and others.
Think of questions, you have to answer more than data, if you have clear question, you can answer using different datas. its not data that is important today, it is the question and ways to solve.
Hope you had solved your problem!
I would like to ask for your help. you said you performed linkage analysis using merlin with whole-exome sequencing data. Well, the whole-exome sequencing data usually presented as .vcf file and the position of variants are located by chromosome position like chr1: 23040402.
But in merlin's map file, the position of variants should be located by centiMorgan.
So, how did you convert the vcf file? Or there any choice to make merlin allow chromosome position as input?
Thank you
Hi Tianyu Lian,
I used Linkdatagen to create Merlin input files. I didn't come across any such issue. You can give it a try. Hope that solves your problem.
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