What is the best tool for association analysis for indels ?

Question

[NB]

Hello,

I have some genotype data that include insertions and deletions apart from rare variants. What is the best method to do an association analysis for indels?

Many thanks

Answer 1

[natasha.sernova]

There were several articles or reports about that.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075619

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4067555/

http://varianttools.sourceforge.net/Association/HomePage

Also this one: http://bib.oxfordjournals.org/content/early/2013/01/21/bib.bbs086.full

There was also a biostar-post:

Illumina Ngs Test Data For Snp/Indel Calling And Association Study

[NB]

Thank you, I think VAT should work for my GWAS genotype data

[natasha.sernova]

See also this papers, they look suitable to your needs.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661514/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4067555/ - the second link in my previous list