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GotCloud: GenomeSTRiP Pipeline (view source)

Revision as of 14:18, 10 February 2015

28 bytes removed ,  14:18, 10 February 2015
→‎Running GotCloud/GenomeSTRiP
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  gotcloud genomestrip --run-metadata --conf gotcloud.conf --outdir outputDirectory --numjobs 10
 
  gotcloud genomestrip --run-metadata --conf gotcloud.conf --outdir outputDirectory --numjobs 10
   −
The metadata pipeline may take a long time to run:
+
Timing:
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* Chromosomes 21 & 22 for 10 BAMs took 1 hour to run with 10 jobs
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* 10 BAMs, chr 21 and 22: 1 hour, 20 mins with 10 jobs
 
* May take a few weeks to run whole genome on 2,000 BAMs
 
* May take a few weeks to run whole genome on 2,000 BAMs
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Timing:
 
Timing:
−
* 10 BAMs, chr 21 and 22: 1 hour, 20 mins
+
* 10 BAMs, chr 21 and 22: 1 hour, 20 mins with 10 jobs
    
=== Genotyping Pipeline ===
 
=== Genotyping Pipeline ===
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  gotcloud genomestrip --run-genotype --conf gotcloud.conf --outdir outputDirectory --numjobs 10
 
  gotcloud genomestrip --run-genotype --conf gotcloud.conf --outdir outputDirectory --numjobs 10
 
Timing:
 
Timing:
−
* 10 BAMs, chr 21 and 22: 4 mins
+
* 10 BAMs, chr 21 and 22: 4 mins with 10 jobs
    
=== 3rd-party Site Genotyping/Filtering Pipeline ====
 
=== 3rd-party Site Genotyping/Filtering Pipeline ====
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12806"

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