README.txt

NAVIP has three existing modules:
 1) VCF preprocessing,
 2) the NAVIP main program,
 3) a simple first analysis of the generated data.

You can choose the module with "--mode <module>".
The module shortcuts are "pre", "main", and "sfa".


VCF preprocessing needs two arguments:
 "--invcf <path_with_file>" and "--outpath <path_to_folder>"

Please be aware, that no new folder will be created.

The NAVIP main program needs four arguments:
 "--invcf <path_with_file>", "--ingff <path_with_file>", "--infasta <path_with_file>", and "--outpath <path_to_folder>"

The best possible output will be available, when the VCF file is 'corrected' by the preprocessing.
However, NAVIP will still be able to deal with most of the 'normal' VCF data and will do its best.

The SFA module needs three arguments:
 "--innavipvcf <path_with_file>", "--innavipfasta <path_with_file>", and "--outpath <path_to_folder>"


Example: VCF preprocessing
python3 navip.py \
 --mode pre \
 --invcf /.../small_variants.vcf \
 --outpath /.../VCF_Preprocessing/

Example: NAVIP main
python3 navip.py \
 --mode main \
 --invcf VCF_Preprocessing/first.vcf \
 --ingff /.../Araport11_GFF3_genes_transposons.201606.gff \
 --infasta /.../TAIR10.fa \
 --outpath /.../NAVIP_Main_Output/

Example: SFA
python3 navip.py \
 --mode sfa \
 --innavipvcf /.../All_VCF.vcf \
 --innavipfasta /.../all_transcripts_data.fa \
 --outpath /.../SFA_Output/