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Revision as of 23:27, 18 May 2015
, 23:27, 18 May 2015→Running GotCloud/GenomeSTRiP 3rd-party Site Genotyping/Filtering Pipeline
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.
${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
This will take ~1 minute to finish.
This will take ~1 minute to finish.
You can also check the output by running
You can check the output by running
zless $OUT/sv/thirdparty/genotype.vcf.gz
zless $OUT/sv/thirdparty/genotype.vcf.gz
