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NAVIP

NAVIP has three existing modules

1. VCF preprocessing
2. NAVIP main program
3. simple first analysis (SFA) of the generated annotation

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

VCF preprocessing needs two more arguments:

"--invcf <path_with_file>" and
"--outpath <path_to_folder>"

Please be aware that no new folder will be created thus the output folder needs to be created manually.

The NAVIP main program needs four arguments:

"--invcf <path_with_file>"
"--ingff <path_with_file>"
"--infasta <path_with_file>"
"--outpath <path_to_folder>"

The best output will be achieved based on a 'corrected' VCF file after running the preprocessing module. However, NAVIP will still be able to deal with most of the 'normal' VCF data sets and will do its best.

The SFA module needs two arguments:

"--innavipvcf <path_with_file>" and
"--outpath <path_to_folder>"
optional:
"--ecc" without any parameter.
"--format <formats>" with PNG,PDF,PS,EPS, and SVG as possible formats. The default is PDF.
"--max_x_axis_bpr <int>" Default parameter is 100.

Examples

VCF preprocessing

"python3 navip.py
--mode pre
--invcf /.../small_variants.vcf
--outpath /.../VCF_Preprocessing/"

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/"

SFA

"python3 navip.py
--mode sfa
--innavipvcf /.../All_VCF.vcf
--outpath /.../SFA_Output/
--format pdf,svg,png"