# HG changeset patch
# User devteam
# Date 1385330988 18000
# Node ID ad50c257e758f7a6456824e8b37ac41013f8d67d
Uploaded
diff -r 000000000000 -r ad50c257e758 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sun Nov 24 17:09:48 2013 -0500
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diff -r 000000000000 -r ad50c257e758 vcftools_compare.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_compare.xml Sun Nov 24 17:09:48 2013 -0500
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+ multiple VCF datasets
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+ tabix
+ vcftools
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+ ## Preprocessing for each dataset.
+ #set dataset_names = []
+ #for $input in $inputs:
+ ## Sort file.
+ sort -k1,1 -k2,2n ${input.file} > ${input.name}.vcf.sorted ;
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+ ## Compress.
+ bgzip ${input.name}.vcf.sorted ;
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+ ## Index.
+ tabix -p vcf ${input.name}.vcf.sorted.gz ;
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+ #silent dataset_names.append( str($input.name) + '.vcf.sorted.gz' )
+ #end for
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+ ## Compare and use sed to simplify output.
+ vcf-compare -w ${window} ${ignore_indels} #echo ' '.join( dataset_names )# | sed 's/\.vcf\.sorted\.gz//g' > ${output}
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+ Please see the VCFtools `documentation`__ for help and further information.
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+ .. __: http://vcftools.sourceforge.net/docs.html
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