Mercurial > repos > ulfschaefer > phephenix

changeset 15:48c41c6ad84e draft

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Uploaded
author ulfschaefer
date Mon, 11 Jul 2016 10:50:16 -0400
parents 2e5a83c0f78f
children 55bfe9d1888e
files filter_vcf.xml
diffstat 1 files changed, 19 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- 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>