# HG changeset patch # User devteam # Date 1401813586 14400 # Node ID d31417e25765a925e1cfd77145fb779a6d191094 # Parent 5c3984014c07d7abd4986c6bd00fedf51cfe73bb Uploaded diff -r 5c3984014c07 -r d31417e25765 pileup_parser.xml --- a/pileup_parser.xml Tue Aug 20 11:07:42 2013 -0400 +++ b/pileup_parser.xml Tue Jun 03 12:39:46 2014 -0400 @@ -320,7 +320,7 @@ 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 +.. image:: pileup_parser_help1.png Running the tool with these parameters will return:: @@ -336,7 +336,7 @@ 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 +.. image:: pileup_parser_help2.png will report everything from the original file:: @@ -355,7 +355,7 @@ 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 +.. image:: pileup_parser_help3.png will produce this:: @@ -371,7 +371,7 @@ Setting **Print quality and base string?** to **Yes** as shown here: -.. image:: ${static_path}/images/pileup_parser_help4.png +.. image:: pileup_parser_help4.png will produce this:: diff -r 5c3984014c07 -r d31417e25765 pileup_parser_help1.png Binary file pileup_parser_help1.png has changed diff -r 5c3984014c07 -r d31417e25765 pileup_parser_help2.png Binary file pileup_parser_help2.png has changed diff -r 5c3984014c07 -r d31417e25765 pileup_parser_help3.png Binary file pileup_parser_help3.png has changed diff -r 5c3984014c07 -r d31417e25765 pileup_parser_help4.png Binary file pileup_parser_help4.png has changed