Changes between Version 54 and Version 55 of SnpCallingPipeline


Ignore:
Timestamp:
Nov 8, 2010 9:36:48 AM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v54 v55  
    7070                color=lightgrey;
    7171
    72                 "sample.aligned.bam" -> "TODO compare against arrays and BGI output"
     72                "sample.aligned.bam" -> "UnifiedGenotype (without realign)"->"QC against arrays and BGI"
    7373
    7474                label = "QC per sample";
     
    9292Todo:
    9393
    94 * Recode workflow 2 to work per genome instead of per chromosome
    95 * QC pipeline
    96    * Simple SNP caller
     94First:
     95* Recode workflow 2 to work per genome instead of per chromosome and test - Freerk
     96* Run on pilot data (6) to evaluate timing and concurrency issues (can 6 run on one node?) - Freerk
     97* Complete analysis of data (60) until including merge to sample.aligned.bam - Freerk
     98* QC pipeline - Can we get Jeroen and Yurii involved here
     99   * UnifiedGenotyper without realign - Freerk
    97100   * GATK variant eval to make venn diagrams
    98    * Contact Yurii for this; Let Jeroen take charge?
     101   * Contact Yurii for this; Let Jeroen take charge?
     102* Share data with Grid following plan Silvia - Freerk
     103* Contact BGI for sample list - Morris
     104* Put report on FTP - Ger,Freerk
    99105
     106Next:
     107* Short tutorial howto generate pipeline scripts - Morris
     108   * Teach Barbara and Jeroen
     109* Port pipeline to Grid with help of Barbara
     110   * What do we need to generate exactly - Barbara
    100111== List of steps ==
    101112