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SnpSift Intervals (version 4.3+t.galaxy0)
Variant input file in VCF format:
Intervals (BED file):
Exclude Intervals:
Filter out (exclude) VCF entries that match any interval in the BED files
You can filter using intervals (BED file).
For details about this tool, please go to:
http://snpeff.sourceforge.net/SnpEff_manual.html
http://snpeff.sourceforge.net/SnpSift.html#intervals