.. _examples:

========
Examples
========

This chapter contains several examples for the most important use cases of VCFPy.

Reading VCF Files
=================

The following is an example for reading VCF files and writing out a TSV file with the genotype calls of all SNVs.
You can find the example Python and VCF file in the sources below the directory ``examples/vcf_to_tsv``.

.. literalinclude:: ../examples/vcf_to_tsv/vcf_to_tsv.py
    :language: python

The program call looks as follows.

.. literalinclude::  ../examples/vcf_to_tsv/stdout.txt
    :language: shell

Writing VCF Files
=================

The following shows how to add values to the ``FILTER`` column to records of an existing VCF file.
Adding to existing records is simpler than constructing them from scratch, of course.

.. literalinclude:: ../examples/add_filter/add_filter.py
    :language: python

The program call looks as follows.

.. literalinclude::  ../examples/add_filter/stdout.txt
    :language: shell

Jumping in Tabix-indexed Files
==============================

The following shows a small program that extracts a genomic region from the input VCF file and writes it to stdout.

.. literalinclude:: ../examples/fetch_tabix/fetch_tabix.py
    :language: python

The program call looks as follows.

.. literalinclude::  ../examples/fetch_tabix/stdout.txt
    :language: shell