Changes between Version 50 and Version 51 of SnpCallingPipeline


Ignore:
Timestamp:
Nov 8, 2010 9:05:17 AM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v50 v51  
    3535                style=filled;
    3636                color=lightgrey;
     37
    3738                "reference.fasta" -> RealignerTargetCreator -> "realign.intervals"
    3839                "indelcalls.vcf"-> RealignerTargetCreator
     
    5152                "flowcell_lane.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> "IndelRealigner & \n FixMateInformation (knownsOnly)" ->"Quality Recalibration"->"flowcell_lane.aligned.bam"
    5253                "realign.intervals" -> "IndelRealigner & \n FixMateInformation (knownsOnly)"   
    53                 label = "Per Lane*Chromosome (750*3*24=54k) ";
     54                label = "Per Lane (750*3=2250) ";
    5455        }
    5556
     
    6970}}}
    7071
     72Discussion
     73
     74* How long takes alignment per genome?
     75   * If this takes very long we can split read files
     76* How long takes realign knownsonly (per genome)?
     77   * If very long, we need to rewrite workflow 2 to split before realign
     78* For realign: if we split per chromosome, can we also split bam file?
     79* How to easily lift over from b36 to b37
     80  * Contact BGI if they can use b37??
     81
     82Todo:
     83
     84* Recode workflow 2 to work per genome instead of per chromosome
     85
    7186== List of steps ==
    7287