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, 13:02, 10 February 2015
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| * Chromosomes 21 & 22 for 10 BAMs took 1 hour to run with 10 jobs | | * 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 | | * May take a few weeks to run whole genome on 2,000 BAMs |
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| + | === Discovery Pipeline === |
| + | The discovery pipeline performs variant discovery across all samples as well as variant filtering based on expert knowledge. |
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| + | gotcloud genomestrip --run-discovery --conf gotcloud.conf --outdir outputDirectory --numjobs 10 |
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| + | === Genotyping Pipeline === |
| + | The genotyping pipeline iterates the discovered variants across the samples, calculating the genotype likelihood for each possible genotype. |
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| + | gotcloud genomestrip --run-genotype --conf gotcloud.conf --outdir outputDirectory --numjobs 10 |
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| + | === 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. |
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| + | gotcloud genomestrip --run-thirdparty --in-vcf 1kg.phase1.chr22.36Mb.sites.vcf --conf gotcloud.conf --outdir outputDirectory --numjobs 10 |