# HG changeset patch
# User ulfschaefer
# Date 1468248616 14400
# Node ID 48c41c6ad84e7377c526709d0f78e42c9efe344b
# Parent  2e5a83c0f78fbd3c684ac3f5a3ba9cb7e5b15625
Uploaded

diff -r 2e5a83c0f78f -r 48c41c6ad84e filter_vcf.xml
--- a/filter_vcf.xml	Fri Jul 01 06:09:01 2016 -0400
+++ b/filter_vcf.xml	Mon Jul 11 10:50:16 2016 -0400
@@ -115,5 +115,24 @@
 
 \-\-only-good           Write only variants that PASS all filters (default all variants are written).
 
+-----
+
+Which filter can be used for your data depends on the variant caller that was used to create the VCF file.
+
+=============  ===============================================
+Filter         Remark
+=============  ===============================================
+GQ score       Always available*
+DP4 ratio      Samtools mpileup before version 1.3 only*
+AD ratio       GATK and samtools mpileup from version 1.3 only
+MQ score       Always available*
+Minimum depth  Always available*
+MQ0 ratio      GATK only
+Quality score  Always available*
+MQ0F ratio     Samtools mpileup only*
+=============  ===============================================
+
+Filters marked with * are availabe for the workflow included with PHE Phenix.
+
   </help>
 </tool>