comparison pileup_parser.xml @ 1:1670f0565000 draft

Uploaded tool help images.

0:ff1ba9b75337

 chrM  414  C  4     ..Ta     III2
 chrM  415  C  4     TTTt     III7
 
To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:

.. image:: ${static_path}/images/pileup_parser_help1.png 

Running the tool with these parameters will return::

 chrM  413  G  4  ..t,  IIIH  0  0  0  1  3
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3

**Example 2**: Report everything

In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:

.. image:: ${static_path}/images/pileup_parser_help2.png 

will report everything from the original file::

 chrM  412  A  2  .,    II    2  0  0  0  2
 chrM  413  G  4  ..t,  III2  0  0  2  1  3

**Example 3**: Report everything and print total number of differences

If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this:

.. image:: ${static_path}/images/pileup_parser_help3.png

will produce this::

 chrM  412  A  2  .,    II    2  0  0  0  2  0
 chrM  413  G  4  ..t,  III2  0  0  2  1  3  1

**Example 4**: Report everything, print total number of differences, and ignore qualities and read bases

Setting **Print quality and base string?** to **Yes** as shown here:

.. image:: ${static_path}/images/pileup_parser_help4.png

will produce this::

 chrM  412  A  2  2  0  0  0  2  0
 chrM  413  G  4  0  0  2  1  3  1

1:1670f0565000

 chrM  414  C  4     ..Ta     III2
 chrM  415  C  4     TTTt     III7
 
To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:

.. image:: pileup_parser_help1.png 

Running the tool with these parameters will return::

 chrM  413  G  4  ..t,  IIIH  0  0  0  1  3
 chrM  414  C  4  ..Ta  III2  0  2  0  1  3

**Example 2**: Report everything

In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:

.. image:: pileup_parser_help2.png 

will report everything from the original file::

 chrM  412  A  2  .,    II    2  0  0  0  2
 chrM  413  G  4  ..t,  III2  0  0  2  1  3

**Example 3**: Report everything and print total number of differences

If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this:

.. image:: pileup_parser_help3.png

will produce this::

 chrM  412  A  2  .,    II    2  0  0  0  2  0
 chrM  413  G  4  ..t,  III2  0  0  2  1  3  1

**Example 4**: Report everything, print total number of differences, and ignore qualities and read bases

Setting **Print quality and base string?** to **Yes** as shown here:

.. image:: pileup_parser_help4.png

will produce this::

 chrM  412  A  2  2  0  0  0  2  0
 chrM  413  G  4  0  0  2  1  3  1