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GotCloud: GenomeSTRiP Pipeline

886 bytes added, 12:02, 10 February 2015
Running GotCloud/GenomeSTRiP
* Chromosomes 21 & 22 for 10 BAMs took 1 hour to run with 10 jobs
* May take a few weeks to run whole genome on 2,000 BAMs
 
 
=== Discovery Pipeline ===
The discovery pipeline performs variant discovery across all samples as well as variant filtering based on expert knowledge.
 
gotcloud genomestrip --run-discovery --conf gotcloud.conf --outdir outputDirectory --numjobs 10
 
 
=== Genotyping Pipeline ===
The genotyping pipeline iterates the discovered variants across the samples, calculating the genotype likelihood for each possible genotype.
 
gotcloud genomestrip --run-genotype --conf gotcloud.conf --outdir outputDirectory --numjobs 10
 
=== 3rd-party Site Genotyping/Filtering Pipeline ====
The third-party genotyping and filtering pipeline performs genotyping on the variant sites specified by an input (3rd-party site) VCF and also performs variant filtering.
 
gotcloud genomestrip --run-thirdparty --in-vcf 1kg.phase1.chr22.36Mb.sites.vcf --conf gotcloud.conf --outdir outputDirectory --numjobs 10

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