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July, 2018:

Repost: Correcting genotyping errors when constructing genetic maps from genotyping by sequencing — GBS — data.

Editor’s note: this is a repost of an article which originally ran on James and the Giant Corn March 26th, 2017. I’m choosing to post this new, slightly amended version a little more than a year later to mark the publication of the paper describing Genotype Corrector. All told it took approximately 18 months from initial submission to final publication. However, to be fair a lot of that time was spent waiting for a single round of peer review at a different journal from the one in which the paper finally appeared.  

When doing anything even vaguely related to quantitative genetics I would chose more missing data over more genotyping errors any day of the week. There are lots of approaches to making missing data less of a pain. The most straightforward of these is called imputation. Imputation essentially means using the genetic markers where you do have information to guess what the most likely genotypes would be at the markers where you don’t have any direct information on what the genotype is. This is possible because of a phenomenon known as linkage disequilibrium or “LD.” Both imputation and LD deserve their own entire write ups and they are on the list of potential topics for when I have another slow Sunday afternoon. For now the  only thing you have to know about them is that, when information on a specific genetic marker is missing, it is often possible to guess with fairly high accuracy what that missing information SHOULD be. But when the information on a specific genetic marker is WRONG… well it’s usually a bit more of a mess (but I think the software solutions for this are getting better! Details at the end of the post.)

Figure 1: Genotype calls along chromosome 1 for six recombinant inbred lines (RILs).

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