We need to start thinking about genome analysis as haplotype reconstruction- not variant calling
We need to start thinking about genome analysis as haplotype reconstruction- not variant calling. 5/5— Deanna Church (@deannachurch) June 20, 2017
Using new technology like linked reads or long reads it is becoming much easier to identify haplotypes in genomes, ie. collections of phased variants.
Can these haplotypes be used for association testing with phenotypes (e.g. qtl mapping, gwas, genomic selection) instead of SNPs? And is there any benefit to using haplotypes? Or will the future of association testing stay with SNPs?
Are there any good articles on this?