What is the best tool for association analysis for indels ?

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

indels association-analysis

• 3,360 views • link

updated 3.2 years ago by Ram

• written 10.2 years ago by NB

1 answer

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

• 0 views • link

written 10.2 years ago by natasha.sernova

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

• 0 views • link

written 10.2 years ago by NB

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

• 0 views • link

written 10.2 years ago by natasha.sernova

More posts like this

How to perform Linkage Disequilibrium (LD) analysis in INDELS
written 1.5 years ago by Ant •

Hello, I am new to studying haplotype associations and am looking for guidance on performing LD analysis on INDELs. I want to conduct SNP association …
Tools to call structural variants in haploid yeast from WGS data
written 2.0 years ago by Tasneem Fetian •

Hello, I have Illumina short-read PE (2x150bp) whole-genome sequencing data from *Saccharomyces cerevisiae*. I have ~40 samples from different mutants and I want to call …
Extract number of INDELs of a specific position for bam file or IGV
written 5.9 years ago by igit_b •

I'm working with Nanopore data that naturally has a lot of INDELs. Is there a way to get all the deletions/insertions from a specific position …
Gene-based common and rare variant association analysis
written 6.9 years ago by seta

Dear all, I’m going work on a given gene with about 170 variants derived from whole genome sequencing of a population (unrelated and related individuals). …
Unit-testing for NGS data analysis pipeline
written 8.5 years ago by NB

Hello, I was wondering if anyone does unit-testing for NGS pipeline that follows GATK best practice and is written in bash ? From what I …
Rare variant analysis
written 8.8 years ago by Sharon

I started doing some rare variant association analysis tests like burden tests and other types. Some methods say whether it suits risk-increasing and risk-decreasing variants …
how to distinguish between artifacts and real indels?
written 9.4 years ago by genya35 •

Hello, I’m working with multiple sequences (fasta format) of the same human gene (exons 2,3,4). Each sequence is about 5300 nucleotides long. When I import …
include indels along with SNPs in linear model
written 10.5 years ago by avari

I am currently preprocessing data from the Illumina PsychArray chip. This chip includes normal tag SNPs and well as other genetic variants such as indels. …
Association study with many types of variants
written 10.7 years ago by weiyuchung •

Hi all, There are many developed methods for specific variant (e.g. SNPs, Indels or CNVs) in association study. However, the disease may not just be …
Why Is The Snp Info Missing From Dbsnp ?
written 13.1 years ago by NB

Hello, In dbSNP some variants like rs71263230,rs28399500,rs52830374 do not have information for the amino acid substitution or function but when you upload the same variants …