search

halasadi / MAPS

software for the MAPS method
MIT License
24 stars 6 forks source link

Help with MAPS #15

Open marlama opened 5 years ago

marlama commented 5 years ago

Dear Al-Asadi,

I'm Marla Mendes, PhD Student from Brazil and I'm trying to use MAPS with my IBD data but I'm having some problems.

If you can help me, my first problem is because my data is the output of RefinedIBD, so they already have the lengh in centimorgans and no gaps (because after Refined IBD I use the Browning and Browning's program merge.ibd). So, for my case I'm trying not use your step Convert_to_cM, and adapted your script to convert BEAGLE output to a .sims file. Do you agree with it or do you have another option for this situation?

Second, the output of your script example_beagle_to_sims.R, gave me the double of lines than the numeber of samples even if I try with you example data. Do you know why this occours?

Thank you for your time!

Regards!

halasadi commented 5 years ago

Sorry for the late response!

1) I agree with your solution. Since your output is already in cM, you don't need the step Convert_to_cM.

2) This occurs because MAPS requires haploid data. Since there are 2x of chromosomes per individual, number of haploids will be double the amount of samples.