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Create workflow specs for STRUCTURE (QC sub-workflow) #4

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ngaddis opened this issue Feb 24, 2020 · 0 comments

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ngaddis commented Feb 24, 2020 •

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Overview of process:

Allow user-specified ancestry thresholds in config
Remove chrX
Genotype call rate filter
Remove ambiguous variants, strand check, and flipping
LD pruning
SNP subset selection
Input data format processing
Run STRUCTURE w/1KGP3 or HapMap
Create STRUCTURE plots for each ancestry based on self-report
Save standard STRUCTURE output and recommended list of samples based on pre-defined cutoffs

ngaddis assigned bryancquach and ngaddis

ngaddis changed the title ~~Create workflow specs for STRUCTURE~~ Create workflow specs for STRUCTURE (QC sub-workflow)

ngaddis mentioned this issue

Create workflow specs for QC of genotype array data #3

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