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berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.
MIT License
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Possible error in SNP coloring #49

Closed ghost closed 7 years ago

ghost commented 7 years ago

When running YJBT07 with YJBT08 as parent chr2 is haploid and there is an area in the middle that is white, we should check if it supposed to be that way image

darrenabbey commented 7 years ago

It isn't clear from your description what the problem is. White in this figure would represent a homozygous region in the parent dataset, which won't necessarily be found in SC5314.

Overall, the figure illustrates a very high quality dataset.

On Sep 27, 2016 2:43 AM, "GuyKha" notifications@github.com wrote:

When running YJBT07 with YJBT08 as parent chr5 is trisomic and there is an area in the middle that is white, we should check if it supposed to be that way [image: image] https://cloud.githubusercontent.com/assets/20476730/18864478/2f7bfb16-849f-11e6-91fc-61a9f0c795b1.png

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vladimirg commented 7 years ago

We should look at the parent to check if that problematic region was homozygous in the parent. If it was, we do not expect it to be colored red, as there was no allelic ratio change from the homozygous diploid parent to the haploid child in this region.

ghost commented 7 years ago

I have checked the issue, the parent is indeed homozygous in this region. Closing