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Revision as of 02:37, 10 December 2014
, 02:37, 10 December 2014→Running GotCloud/GenomeSTRiP Metadata Pipeline
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}
'''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'''.
Instead, let's look what the output would have looked like.
Instead, let's look what the output would have looked like.
ls ${SS}/svtoolkit/metadata
ls ${OUT}/sv/metadata
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
