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Running GotCloud/GenomeSTRiP Metadata Pipeline
In principle, the metadata can be created from the input BAM files by running the following command
perl ${SSGC}/svtoolkit/bin/ -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'''.
Instead, let's look what the output would have looked like.
ls ${SSOUT}/svtoolkitsv/metadata
cpt depth depth.dat gcprofile genome_sizes.txt isd isd.dist.bin spans spans.dat