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Revision as of 18:17, 27 June 2014
, 18:17, 27 June 2014→Running GotCloud/GenomeSTRiP Genotyping Pipeline
The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.
The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.
time perl $GC/bin/genomestrip.pl -run-genotype --metadata $IN/metadata --out $OUT/sv --conf $IN/gotcloud.conf --region 22:36000000-37000000 --numjobs 4
time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-genotype --metadata ${SS}/svtoolkit/metadata --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT}
This will take ~3 minutes to finish.
This will take ~3 minutes to finish.
