Changes between Version 19 and Version 20 of SnpCallingPipeline


Ignore:
Timestamp:
Oct 16, 2010 5:53:51 PM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline

    v19 v20  
    2323                "reference.fasta" -> RealignerTargetCreator -> "realign.intervals"
    2424                "indelcalls.vcf"-> RealignerTargetCreator
     25                "reference.fasta"->Split->"chr[1-24].fasta"
    2526                dbsnp -> RealignerTargetCreator
    2627                label = "Per genome";
     
    3233                node [style=filled,color=white];
    3334                "Reads.1fq.gz" -> align1 -> alignPE
    34                 "reference.fasta"->Split->"chrN.fasta" -> align1
    35                 "chrN.fasta" -> align2
    36                 "chrN.fasta" -> alignPE
     35                "chr[1-24].fasta" -> align1
     36                "chr[1-24].fasta" -> align2
     37                "chr[1-24].fasta" -> alignPE
    3738                "Reads.2.fq.gz" -> align2 -> alignPE -> MarkDuplicates -> RealignIndelsAndFixMates -> "Lane.aligned.bam"
    3839                "realign.intervals" -> RealignIndelsAndFixMates   
    39                 label = "Per lane";
     40                label = "Per lane/Per chromosome";
    4041        }
    4142
     
    4950                RealignIndelsAndFixMates2 -> IndelGenotyperV2 -> FilterSingleCalls -> UnifiedGenotyper -> Filtration -> VariantEval -> "QC reports"
    5051Filtration -> VCF
    51                 label = "Per Sample";
     52                label = "Per Sample/Per Chromosome";
    5253        }
    5354