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, 23:27, 18 May 2015
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| You can take a 3rd-party site and genotype with GenomeSTRiP. Here we take a 1000 Genomes phase 1 sites and genotype them. | | You can take a 3rd-party site and genotype with GenomeSTRiP. Here we take a 1000 Genomes phase 1 sites and genotype them. |
− | * If running on a small machine, you may want to reduce <code>--numjobs</code> from 4 to 1. | + | * If running on a small machine, you may want to reduce <code>--numjobs</code> from 8 to 1. |
− | perl ${GC}/bin/genomestrip.pl --run-thirdparty --in-vcf ${SS}/ext/1kg.phase1.chr22.36Mb.sites.vcf --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --numjobs 2 | + | ${GC}/gotcloud genomestrip --run-thirdparty --in-vcf ${SS}/ext/1kg.phase1.chr22.36Mb.sites.vcf --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --numjobs 8 |
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| This will take ~1 minute to finish. | | This will take ~1 minute to finish. |
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− | You can also check the output by running | + | You can check the output by running |
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| zless $OUT/sv/thirdparty/genotype.vcf.gz | | zless $OUT/sv/thirdparty/genotype.vcf.gz |