Hi

I have a few questions regarding genotype imputation using Beagle.

I am very new in the bioninformatics field, so forgive me if I am asking any dumb questions.

1. Can anyone post here an example of a genotype imputation command line? I don't know if I am doing it right.

2. Regarding the markers file. I am using SVS to prepare my data.

   a. Do I necessarily need to apply a markers map to my data before exporting it to beagle?

   b. how do I create a markers file for beagle?

I have two files: one with genotype data for a group of sires (30 individuals) genotyped using a 770K markers chip, and another one with the offspring for those sires (around 804) genotyped using a 50K markers chip

The sires will be used to impute the offspring

So, I need to have in my markers file only the list of markers used to gneotype the sires. How do I filter this data and how do I create this marker file?

If you can explain me using a very simple language and give me examples of commands I should be using that would be very helpful.

I am very new in the field and am pretty lost!

Thank you in advance