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16 bytes removed
, 02:37, 10 December 2014
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| In principle, the metadata can be created from the input BAM files by running the following command | | In principle, the metadata can be created from the input BAM files by running the following command |
− | perl ${SS}/svtoolkit/bin/genomestrip.pl -run-metadata --conf ${SS}/gotcloud.conf --numjobs 2 --base-prefix ${SS} --outdir ${OUT} | + | perl ${GC}/bin/genomestrip.pl -run-metadata --conf ${SS}/gotcloud.conf --numjobs 2 --base-prefix ${SS} --outdir ${OUT} |
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| '''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take ~50 minutes to finish'''. | | '''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take ~50 minutes to finish'''. |
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| Instead, let's look what the output would have looked like. | | Instead, let's look what the output would have looked like. |
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− | ls ${SS}/svtoolkit/metadata | + | ls ${OUT}/sv/metadata |
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| cpt depth depth.dat gcprofile gcprofiles.zip genome_sizes.txt isd isd.dist.bin spans spans.dat | | cpt depth depth.dat gcprofile gcprofiles.zip genome_sizes.txt isd isd.dist.bin spans spans.dat |