# HG changeset patch # User devteam # Date 1385310084 18000 # Node ID 2df3463828ff46b892092d80f9bf95b2a9a73ccc Uploaded diff -r 000000000000 -r 2df3463828ff tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Nov 24 11:21:24 2013 -0500 @@ -0,0 +1,6 @@ + + + + + + diff -r 000000000000 -r 2df3463828ff vcftools_merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools_merge.xml Sun Nov 24 11:21:24 2013 -0500 @@ -0,0 +1,52 @@ + + multiple VCF datasets + + + vcftools + + + + ## Preprocessing for each dataset. + #set dataset_names = [] + #for i, $input in enumerate( $inputs ): + ## Sort file. + vcf-sort ${input.file} > ${i}.vcf.sorted ; + + ## Compress. + bgzip ${i}.vcf.sorted ; + + ## Index. + tabix -p vcf ${i}.vcf.sorted.gz ; + + #silent dataset_names.append( str($i) + '.vcf.sorted.gz' ) + #end for + + ## Merge. + vcf-merge + #echo ' '.join( dataset_names ) # > ${output} + + + + + + + + + + + + + + + + + + + + + + Please see the VCFtools `documentation`__ for help and further information. + + .. __: http://vcftools.sourceforge.net/docs.html + +