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Old 02-02-2011, 05:44 PM   #2
Michael.James.Clark
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Location: Palo Alto

Join Date: Apr 2009
Posts: 213
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Some of the VCFtools seem to only work with uncompressed or compressed files. Another example I found is the --remove-filtered <string> and --keep-filtered <string>, which were only working with uncompressed files for me.

As for your ZCAT problem, Mac OS X's version of ZCAT demands that the file end in .Z. I was under the impression the latest VCFtools fixed this issue but if not, you can just move the files and append a .Z on the end for the sake of merging I think.
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