Welcome to DING_log’s documentation!

Contents:

• GBS v2 Pipeline
  • Summary
  • Essential files Overview
    • Q & A
  • Discovery Pipeline Overview
    • Step1 (GBSSeqToTagDBPlugin)
    • Step2 (TagExportToFastqPlugin):
    • Step3 (BWA alingment)
    • Step4 (SAMToGBSdbPlugin)
    • Step5 (DiscoverySNPCallerPluginV2)
    • Step6 (SNPQualityProfilerPlugin)
    • Step7 (UpdateSNPPositionQualityPlugin)
    • Step8 (SNPCutPosTagVerification)
  • Production Pipeline Overview
  • Q & A
• PLINK Recipe
  • Summary
  • How it works
    • What I need here
  • Q & A
  • Introduction and meaning for me
    • Data management
  • Population stratification
• fastStructure
  • 20200122
    • Github-server
• PilotRun
  • 20191113_Step1: GBSSeqToTagDBPlugin
  • 20191118_Step2: TagExportToFastqPlugin
  • 20191118_Step3: Alingment
  • 20191118_Step5: DiscoverySNPCallerPluginV2
  • 20191118_ProductionSNPCallerPluginV2
  • 20191118_Step6: SNPQualityProfilerPlugin
  • 20191120_Step4: SAMToGBSdbPlugin
  • 20191120_Step5: DiscoverySNPCallerPluginV2
  • 20191125_Step6: SNPQualityProfilerPlugin
  • 20191125_Step7: UpdateSNPPositionQualityPlugin
  • 20191123_ProductionPipeline ProductionSNPCallerPluginV2
  • Q & A
  • 20200115_SNP-filter
  • 20200116_UPDATED information
• Diploid
  • 20200115-16_TASSEL-GBS
  • 20200116_SNP-filter
    • Program: TASSEL v5.0 GUI
  • 20200116_PLINK
    • Summary statistics
    • Principal coordinate analysis (PCoA)
    • Summary at this moment
  • 20200116_Bayesian – fastStructure
    • Prepare in PLINK v1.9 – LD-based SNPs
    • Github-server
    • Summary for 0116
  • 2020123_Adjustment-meeting with Alex
  • 20200127-28_SNP filtering
    • Program: PLINK v1.9
    • Results and comments for Jan.27th
    • Rerun Round1 – after reading document
    • Rerun Round2 – worked well
    • Rerun Round more – different filtering conditions
    • Conclusion for SNPs filtering
  • 20200128-31_fastStructure
    • Step1: PLINK v1.9, LD-based SNP pruning (20200128)
    • Step2: run fastStructure (20200128)
    • Summaries - problems & solutions:
  • 20200131_meeting with Alex
  • 20200204_New LD pruning & FS
    • PLINK
    • FS-FastStructure
  • 20200204_R-PCA & DAPC - ‘adegenet’ package in R
    • glPca
  • 20200210_PCoA-PLINK
    • Summaries & questions for PCoA in PLINK
  • 20200210_DAPC-adegenet
  • 20200217_Summaries of DIPLOID-GBS analsis
    • Questions summaries
    • Structure summaries
  • 20200220_F-statistics
    • Data-management
    • FST analysis
    • Summaries
• Tetraploid reference
  • TASSEL-GBS (SNP Calling)
    • Essential files
    • Steps
    • TIME CONSUMED
  • PLINK (SNP Filtering) & DAPC TEST
    • FILTERING
    • DAPC RESULTS
  • TEST DIFFERENT PARAMETERS
    • DAPC RESULTS
    • PHYLOGENY RESULTS
  • ERROR & SOLUTION INFO
• VCFfiles
  • 20200114 VCF2PopTree
  • Basics in VCF Notes
    • References
    • Aims for this notes
    • Basics in VCF
  • VCF file from TASSEL-GBS
    • Header
    • Variant call records

Indices and tables

• Index
• Module Index
• Search Page