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, 17:20, 26 June 2014
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| To discover large deletions from the 62 BAMs we are using for this workshop, you can run the following command | | To discover large deletions from the 62 BAMs we are using for this workshop, you can run the following command |
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− | time perl $GC/bin/genomestrip.pl -run-discovery --metadata $IN/metadata --out $OUT/sv --conf $IN/gotcloud.conf --region 22:36000000-37000000 --numjobs 2 | + | time perl ${GC}/bin/genomestrip.pl -run-discovery --metadata ${SS}/svtoolkit/metadata --out ${OUT}/sv --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --numjobs 2 --gs-dir ${SS}/svtoolkit |
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| This will take ~2 minutes to finish. | | This will take ~2 minutes to finish. |