61
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Analysis of Structural Variation Practical, May 2015 (view source)
Revision as of 18:34, 24 August 2015
, 18:34, 24 August 2015→Running GotCloud/GenomeSTRiP 3rd-party Site Genotyping/Filtering Pipeline: split long command line
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 8 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 --list bams/bam.list
${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 --list bams/bam.list
This will take ~1 minute to finish.
This will take ~1 minute to finish.
