Non Invasive Prenatal Testing (NIPT)

1. Download NIPT package

Download the NIPT package.
Using the terminal, change the files permissions with the following command.
```
chmod 755 -R NIPT-master
```

2. Download the Samtools package

Download the Samtools package, version 1.3.1.

https://sourceforge.net/projects/samtools/files/samtools/1.3.1/
Unzip the Samtools package and put inside the Samtools folder.
Inside the folder Samtools/samtools-1.3.1, run the following commands:
```
./configure
make
```

3. To include a new microhaplotype for analisys

Inside the folder 1000G_test, there are two folders, onde named VCF and other named MICRO.

Put the vcf (obtained from 1000 Genomes) in the folder VCF. Example of vcf name:

4.7447228-7447353.ALL.chr4.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf

Put the microhaplotype's list of SNPs in the folder MICRO. Example of list name:
```
list4.7447228-7447353
```
Call the script 1000G.pl (inside the NIPT folder).
```
./1000G.pl -v 1000G_test/VCF/vcf_name -m 1000G_test/MICRO/list_name -n microhaplotype_number
```
Obs: The microhaplotype number has to be sequencial and composed of two numbers.
The output is a file named MXX_meta_file.txt (where XX = microhaplotype_number).
Put the file MXX_meta_file.txt in the folder Haplotypes.
There is a file named Microhaplotypes.txt inside the folder Files. Add a line in the file with chromosome, start position and end position (chr4:7447228-7447353).
There is a file named SNPs.bed inside the folder Files. Put the SNPs that compose the microhaplotype in bed format (7 columns).

4. To calculate the probability of paternity

Go to the directory where the mother, the plasma and the alleged father's BAM files are located.

Call the script Paternity_Calc.pl

Paternity_Calc.pl -X BAM_alleged_father -Y BAM_mother -Z BAM_plasma

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