Changes between Version 1 and Version 2 of PipelinePlan


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Timestamp:
Sep 6, 2010 8:07:33 PM (11 years ago)
Author:
Morris Swertz
Comment:

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  • PipelinePlan

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    11[[TOC()]]
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    32= Analysis pipeline =
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    54BGI will provide us with SAM/BAM standard formatted files containing the raw, uncleaned reads.  This is the main input for our pipeline.
    6 We will construct a data processing and analysis pipeline, based on the recent experiences from 1000 Genomes Project, using (where available) existing tools already developed (such as GATK, SAMTOOLS, PICARD). See Genome Analysis Pipeline document drafted by Morris for individual steps for alignment, quality score recalibration, indel cleaning. The aim is to compare the outputs (sites called, genotypes called) between this pipeline and BGI.
     5We will construct a data processing and analysis pipeline, based on the recent experiences from 1000 Genomes Project, using (where available) existing tools already developed (such as GATK, SAMTOOLS, PICARD).
     6
     7See Genome Analysis Pipeline document drafted by Morris for individual steps for alignment, quality score recalibration, indel cleaning. The aim is to compare the outputs (sites called, genotypes called) between this pipeline and BGI.
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    89== Action items for pilot data: (URGENT) ==