.. _odgi panpos:

#########
odgi panpos
#########

get the pangenome position of a given path and nucleotide position (1-based)

SYNOPSIS
========

**odgi panpos** [**-i, –idx**\ =\ *FILE*] [**-p, –path**\ =\ *STRING*]
[**-n, –nuc-pos**\ =\ *N*] [*OPTION*]…

DESCRIPTION
===========

The odgi panpos(1) command give a pangenome position for a given path
and nucleotide position. It requires a path index, which can be created
with :ref:`odgi pathindex`. Going
from **path:position** → **pangenome:position** is important when
navigating large graphs in an interactive manner like in the
`Pantograph <https://graph-genome.github.io/>`__ project. All input and
output positions are 1-based.

OPTIONS
=======

Graph Files IO
--------------

| **-i, –idx**\ =\ *FILE*
| File containing the succinct variation graph index to find the
  pangenome position in. The file name usually ends with *.xp*.

Position Options
----------------

| **-p, –path**\ =\ *STRING*
| The path name of the query.

| **-n, –nuc-pos**\ =\ *STRING*
| The nucleotide sequence of the query.

Program Information
-------------------

| **-h, –help**
| Print a help message for **odgi panpos**.

..
	EXIT STATUS
	===========
	
	| **0**
	| Success.
	
	| **1**
	| Failure (syntax or usage error; parameter error; file processing
	  failure; unexpected error).
	
	BUGS
	====
	
	Refer to the **odgi** issue tracker at
	https://github.com/pangenome/odgi/issues.