Post date: Dec 12, 2019 8:39:0 PM
I prepared slides and made a presentation of my project and progress at the lab meeting yesterday. Will forgot that he had lab meeting and did not see my presentation, just the last slide. I however got interesting questions from my team mates who were present, which I will summarize here:
- We used one technique to decide for the true heterozygotes (everything above 80% of heterozygotes per SNP). It would be interesting to confirm this choice with another technique, for example as suggested by Peter: take the true heterozygotes, calculate the Euclidian distance between latitute and longitude - ask him again? I do not remember well...
- We have looked at the increase of heterozygotes so far but it would be interesting to look at the lost of heterozygotes: copies repaired, from hetroZ, some can become homozygotes again, study the heterozygotes that may have begun homozygotes. (Tony)
- What are the parameters used by bcftools to call variants and is this influenced by the assumption the organisms are diploïd? Some parameters would need to be adjusted for triploïds: the 50/50 ratio in a binary world would become 33/33/33... This could biais the evidence with which variants are called, where a site with 4 reads would need to be missed because there would not be enough data to decide. (Tony)
- Merge reads together and imply phylogeny from there.