READ ME FILE 1: Imputation and Haplotype analysis

Creating Tassel files from a .cvs file

1º step: At this point you should have a .cvs file with your genotypes and markers.
Open your file on Tassel, go to Data and then, Sort genotype file. Open this same
file in Input file and give it a new name on Output file. File type has to be
Hapmap. Save.

2º step: Filter your data set by MAF. Go to Filter and choose Sites that means
markers. To do call rate you should use R or other software.

3º step:: Identify duplicates on your files (you can use excel for it) and exclude
it.

Imputing on Beagle
1º step: To install Beagle

How to install Beagle

a. Go to https://faculty.washington.edu/browning/beagle/beagle.html and download

Beagle;

b. Create a folder on C:Users/Iara and extract Beagle on there.

2º step: Use command line to access the folder you created for Beagle. (Use cd to
forward and cd .. to backward).

3º step: Before performing the imputation, the data has to be at the same folder
than Beagle and in a vcf format. Go to Tassel, open your data, click on Impute and
then on Remove indels for input to Beagle v.4. At inFileName you should choose the
same file (data) as well as outFileName. Don't Retain monomorphic sites.

4º step: Go to command line and type the following code:

java -Xmx8000000m -jar beagle.21Sep19.ec3.jar gt=YOUR_FILE_HERE.vcf.gz

out=NAME_OF_OUTPUT_FILE

Obs: gt= file's name, out= output's name

Now you have a imputed file!