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Create workflow specs for STRUCTURE (QC sub-workflow)
#4
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ngaddis
opened
4 years ago
ngaddis
commented
4 years ago
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
Overview of process: