Changes between Version 5 and Version 6 of VCFAggregateScriptManual

Timestamp:

2014-09-17T13:49:07+02:00 (11 years ago)

Author:

jvelde

Comment:

--

VCFAggregateScriptManual

@@ -44 +44 @@
 Afterwards, be sure to inspect the log file for warnings!
 
+{{{
 more stripped.vcf.log
+}}}
 
-Full manual:
+Man page:
 
-Create a summary VCF per batch:
- -ss       : remove sample details!
- -fv PASS  : keep only high quality variant calls that pass all filters applied in NextGene.
-             Just to be sure: variants should already have been filtered on PASS only in a previous step,
-             so this should be redundant here...
- -si       : remove all INFO subfields except for INFO:AN and INFO:AC.
-             INFO:AN and INFO:AC were automatically updated by vcf-merge,
-             but the others were not and may contain erroneous annotation
-             that cause vcf-validator to complain the created VCF is not valid.
- -ll       : specifies log level, e.g. INFO
-
+{{{
+#
+# Create a summary VCF per batch:
+#  -ss       : remove sample details!
+#  -fv PASS  : keep only high quality variant calls that pass all filters applied in NextGene.
+#              Just to be sure: variants should already have been filtered on PASS only in a previous step,
+#              so this should be redundant here...
+#  -si       : remove all INFO subfields except for INFO:AN and INFO:AC.
+#              INFO:AN and INFO:AC were automatically updated by vcf-merge,
+#              but the others were not and may contain erroneous annotation
+#              that cause vcf-validator to complain the created VCF is not valid.
+#
+}}}