Entering edit mode
8 months ago
German.M.Demidov
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2.9k
Dear community members,
I've searched for linkage analysis (in disease context: one has affected, unaffected relatives and wants to find the common loci) on biostars and found many questions (including mine, several years old), but no detailed answer.
Google gives Merlin tool as the first suggestion and the tool was developed in 1999, if I am not mistaken.
Is there a good tutorial on linkage analysis using more modern tools and more modern data (i.e. higher coverage genomes)?
Much appreciated!
While you wait for an answer, here are some packages that seem recent which you may have already found but just in case:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02326-x
https://academic.oup.com/bib/article/22/3/bbaa077/5835558
The 2nd one looks very good (and takes VCFs as input which is already rare) - the 1st is more about organisms without reference, if I understood, so assembly method =) UPD: sorry it is assembly free method, by kmers - still for humans I believe alignment-based methods would be more "interpretable"
unrelated note: crazy but the 2nd tool is web-server only, if I understood correctly - https://mcg.ustc.edu.cn/bsc/pedminer/analysis.html - we're not allowed to upload our clinical VCFs anywhere, sadly =( only stand alone...
Perhaps not what you need but
somalier: https://github.com/brentp/somalierFrom Elixir: https://bio.tools/t?page=1&q=%27Linkage%20analysis%27&sort=score