# HG changeset patch
# User devteam
# Date 1385331057 18000
# Node ID 76ff5512748ce7a574aa65b8191371dad27872be
Uploaded
diff -r 000000000000 -r 76ff5512748c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sun Nov 24 17:10:57 2013 -0500
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diff -r 000000000000 -r 76ff5512748c vcftools_merge.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_merge.xml Sun Nov 24 17:10:57 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 i, $input in enumerate( $inputs ):
+ ## Sort file.
+ vcf-sort ${input.file} > ${i}.vcf.sorted ;
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+ ## Compress.
+ bgzip ${i}.vcf.sorted ;
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+ ## Index.
+ tabix -p vcf ${i}.vcf.sorted.gz ;
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+ #silent dataset_names.append( str($i) + '.vcf.sorted.gz' )
+ #end for
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+ ## Merge.
+ vcf-merge
+ #echo ' '.join( dataset_names ) # > ${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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