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tpbilton / GUSMap

Genotyping Uncertainty with Sequencing data and linkage MAPping
GNU General Public License v3.0
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GUSMap on F2 from pure lines #22

Closed eyalbenda closed 4 years ago

eyalbenda commented 4 years ago

I have F2 from pure homozygote lines. I understand from your paper that GUSMap should be applicable, as equivalent to a full-sib design. I wanted to ask how do I prepare my data and ped file for GUSmap.

tpbilton commented 4 years ago

Hi, yes the methodology in GUSMap should extend easily to F2 populations. I just hadn't got round to implementing this in the software yet. Give me a week and I'll code it up for you.

Thanks, Timothy

eyalbenda commented 4 years ago

That would be fantastic, thanks!

tpbilton commented 4 years ago

One question. Will you have any genotype information on the parents or do you only sequence the F2 progeny since they suppose to only segregate at 1:2:1? I have never had to analyze an F2 population before. I would have thought that if you have the parents (which are homozygous right) that you could determine which base the individuals inherits from their parents, but I'm not sure if this is important or not.

Thanks, Timothy

eyalbenda commented 4 years ago

I have high coverage sequencing of the parental lines P0, who are purely homozygous. I use that to call variants. The F1 are all heterozygote so I don't bother to sequence them. Then I have very low coverage sequencing of F2 progeny (from F1 intercross). I think most people sequence the pure parental lines, and if they work with common model organisms we often work with lines that are already sequenced. Thanks,

Eyal

On Sat, May 16, 2020, 01:42 Timothy Bilton notifications@github.com wrote:

One question. Will you have any genotype information on the parents or do you only sequence the F2 progeny since they suppose to only segregate at 1:2:1? I have never had to analyze an F2 population before. I would have thought that if you have the parents (which are homozygous right) that you could determine which base the individuals inherits from their parents, but I'm not sure if this is important or not.

Thanks, Timothy

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tpbilton commented 4 years ago

Hi Eyal,

I'm still working on updating GUSMap for F2 populations. Sorry about this. Ran into a few bugs that I'm still trying to fix. Will let you know when I'm done.

Thanks, Timothy

eyalbenda commented 4 years ago

Great, thanks so much for the update!

tpbilton commented 4 years ago

Hi Eyal,

Ok, I have uploaded a new version of GUSMap (v2.2.0) today to GitHub. It now has an IC class which should be able to handle an F2 population. Have a read through the IC tutorial to understand how it works.

Note: At this stage, I have decided to not use the grandparental information in GUSMap for F2 populations (since the SNPs are assumed to be segregating with the same ratio). Only the F2 progeny are used to construct the linkage maps.

Let me know if you have any questions or run into any problems.

Thanks, Timothy