# HG changeset patch
# User devteam
# Date 1385308883 18000
# Node ID 937918765b6e9e989ccc35e6d62b9946fa3bfe3d
Uploaded
diff -r 000000000000 -r 937918765b6e tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sun Nov 24 11:01:23 2013 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+
diff -r 000000000000 -r 937918765b6e vcftools_compare.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_compare.xml Sun Nov 24 11:01:23 2013 -0500
@@ -0,0 +1,58 @@
+
+ multiple VCF datasets
+
+
+ tabix
+ vcftools
+
+
+
+ ## Preprocessing for each dataset.
+ #set dataset_names = []
+ #for $input in $inputs:
+ ## Sort file.
+ sort -k1,1 -k2,2n ${input.file} > ${input.name}.vcf.sorted ;
+
+ ## Compress.
+ bgzip ${input.name}.vcf.sorted ;
+
+ ## Index.
+ tabix -p vcf ${input.name}.vcf.sorted.gz ;
+
+ #silent dataset_names.append( str($input.name) + '.vcf.sorted.gz' )
+ #end for
+
+ ## Compare and use sed to simplify output.
+ vcf-compare -w ${window} ${ignore_indels} #echo ' '.join( dataset_names )# | sed 's/\.vcf\.sorted\.gz//g' > ${output}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Please see the VCFtools `documentation`__ for help and further information.
+
+ .. __: http://vcftools.sourceforge.net/docs.html
+
+