diff --git a/docs/content/harvest/quickstart.rst b/docs/content/harvest/quickstart.rst
index b15fb1a..2d69126 100644
--- a/docs/content/harvest/quickstart.rst
+++ b/docs/content/harvest/quickstart.rst
@@ -81,7 +81,28 @@ Primary output files
 
 #. Compressed binary archive (GGR)
 
+Additional output files
+-------------
 
-
+1. Variant Call Format (.vcf))
+   
+  Example VCF output file:  ::
+
+    ##FILTER=<ID=IND,Description="Column contains indel">
+    ##FILTER=<ID=N,Description="Column contains N">
+    ##FILTER=<ID=LCB,Description="LCB smaller than 200bp">
+    ##FILTER=<ID=CID,Description="SNP in aligned 100bp window with < 50% column % ID">
+    ##FILTER=<ID=ALN,Description="SNP in aligned 100b window with > 20 indels">
+    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  England1.fna.ref        Al-Hasa_18_2013.fna     Al-Hasa_1_2013.fna      England-Qatar_2012.fna  KSA-CAMEL-376.fna       NC_019843.2.fna
+    gi|471258596|gb|KC164505.2|     1603    GTACTATGTA.CTTTGTGCCT   C       T       40      PASS    NA      GT      0       0       0       0       1       0
+    gi|471258596|gb|KC164505.2|     1684    GGAACAAGGT.CACTCAAATT   C       T       40      PASS    NA      GT      0       0       0       0       1       0
+    gi|471258596|gb|KC164505.2|     2502    ATATTCCCAT.CGGGAACCTA   C       T       40      PASS    NA      GT      0       0       0       0       1       0
+    gi|471258596|gb|KC164505.2|     3275    TTCTCATGAG.ATTTCTGACG   A       G       40      PASS    NA      GT      0       1       1       0       1       0
+    gi|471258596|gb|KC164505.2|     4396    TTCAAGCAGG.GAGTGTCGTG   G       T       40      PASS    NA      GT      0       1       1       0       0       0
+   
+   .
+   .
+   .
+   
 
 
diff --git a/docs/content/parsnp.rst b/docs/content/parsnp.rst
index 2363a82..a41e7f2 100644
--- a/docs/content/parsnp.rst
+++ b/docs/content/parsnp.rst
@@ -3,6 +3,8 @@ Parsnp
 ======
 **Rapid core genome multi-alignment**
 
+.. image:: parsnp/parsnp_icon_medium.png
+
 Project home page: https://github.com/marbl/parsnp
 
 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
diff --git a/docs/content/parsnp/parsnp_icon_medium.png b/docs/content/parsnp/parsnp_icon_medium.png
new file mode 100644
index 0000000..7bf9da6
Binary files /dev/null and b/docs/content/parsnp/parsnp_icon_medium.png differ
diff --git a/docs/content/parsnp/quickstart.rst b/docs/content/parsnp/quickstart.rst
index 5b775fe..9315aba 100644
--- a/docs/content/parsnp/quickstart.rst
+++ b/docs/content/parsnp/quickstart.rst
@@ -97,10 +97,9 @@ LCB alignment::
  -n = <string>: alignment program (default: libMUSCLE)
  -u = <flag>: output unaligned regions? .unaligned (default: NO)
   
-SNP filters::
+Recombination filtration::
 
- -R = <flag>: enable (R)epeat filtering?
- -x = <flag>: enable recombination filtering? (default: NO)
+ -x = <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO)
   
 Misc::