Update docs for better clarity around removing important filters and …

…using exomiser to annotate and score variants.

docs/advanced_analysis.rst

@@ -320,7 +320,7 @@ Analysis steps are defined in terms of :ref:`variant filters<variantfilters>`, :
 operate on genes but also require the variants to have already been filtered. The optimiser will ensure that these are
 run at the correct time if they have been incorrectly placed.
 
-Using these it is possible to create artificial exomes, define gene panels or only examine specific regions, for example.
+Using these it is possible, for example to create artificial exomes, define gene panels or only examine specific regions.
 
 .. _variantfilters:
 
@@ -414,14 +414,20 @@ frequencyFilter:
 Frequency cutoff of a variant **in percent**. Frequencies are derived from the databases defined in the :ref:`frequencySources<frequencysources>`
 section. We recommend a value below 5.0 % depending on the disease. Variants will be removed/failed if they have a
 frequency higher than the stated percentage in any database defined in the :ref:`frequencySources<frequencysources>` section.
-_n.b_ Not defining this filter will result in all variants having no frequency data, even if the :ref:`frequencySources<frequencysources>`
-contains values.
 
 .. code-block:: yaml
 
     frequencyFilter: {maxFrequency: 1.0}
 
 
+.. important::
+
+    Not defining this filter will result in all variants having no frequency data, even if the :ref:`frequencySources<frequencysources>`
+    are defined. Failing to include this will result in Exomiser assuming variants are all very rare and subsequently
+    assigning an artificially inflated score, especially for very common variants. If you want to score all variants and
+    write failed ones to the output, it is recommended to use `analysisMode: FULL`.
+
+
 .. _pathogenicityfilter:
 
 pathogenicityFilter:
@@ -436,6 +442,14 @@ This filter is meant to be quite permissive and we recommend it be set to true.
     pathogenicityFilter: {keepNonPathogenic: true}
 
 
+.. important::
+
+    Not defining this filter will result in all variants having no pathogenicity data or ClinVar annotations, even if the
+    :ref:`pathogenicitySources<pathogenicitysources>` are defined. Failing to include this will result in Exomiser
+    using default scores based on the assigned variant effect. If you want to score all variants and write failed ones
+    to the output, it is recommended to use `analysisMode: FULL`.
+
+
 .. _genefilters:
 
 Gene filters

docs/input_files_and_options.rst

@@ -78,6 +78,15 @@ genome assembly and is enabled in the ``application.properties`` see the :ref:`r
 Analysis
 ========
 
+.. important::
+
+    The exome and genome analyses found in the `test-analysis-exome.yml` and `test-analysis-genome.yml` files are
+    recommended for use in most situations, and removing steps from the analysis is likely to negatively impact
+    performance. It is *strongly* recommended to test any changes against the standard setup on the example samples and
+    your own solved cases to check the impact of any changes you might want to make. If you want to score all variants
+    and write failed ones to the output, it is recommended to use `analysisMode: FULL`.
+
+
 Analysis files contain all possible options for running an analysis including the ability to specify variant frequency
 and pathogenicity data sources and the ability to tweak the order that analysis steps are performed.
 
@@ -94,14 +103,6 @@ setting the analysisMode option to PASS_ONLY. This will also aid your ability to
 
 Analyses can be run in batch mode. Simply put the path to each analysis file in the batch file - one file path per line.
 
-.. important::
-
-    The exome and genome analyses found in the `test-analysis-exome.yml` and `test-analysis-genome.yml` files are
-    recommended for use in most situations, and removing steps from the analysis is likely to negatively impact
-    performance. It is *strongly* recommended to test any changes against the standard setup on the example samples and
-    your own solved cases to check the impact of any changes you might want to make.
-
-
 .. parsed-literal::
 
     java -jar exomiser-cli-|version|.jar --analysis-batch examples/test-analysis-batch.txt