├── 01.quality control └── shell.sh ├── 02.variants calling └── shell.sh ├── 03.population structure ├── plink.distance.matrix.to.mega.pl └── shell.sh ├── 04.demographic ├── bootstrap_smcpp.py ├── shell.sh └── softmasked_to_bed.py ├── 05.gene flow ├── 03.beagle2treemix.py ├── 04.treemix2geno.pl └── shell.sh ├── 06.ancient DNA ├── 2018-11-17-ancient-DNA-report.pptx └── readme ├── 07.Mitochondrial analysis └── shell.sh ├── 08.selective sweep ├── Merge.SFS.pl ├── XPEHH.window.pl └── shell.sh ├── 09.association study ├── 01.GWAS │ ├── EmmaxFilter.py │ ├── MANHATTAN_QQ.r │ ├── manqqplot.r │ └── shell.sh ├── 02.QTL │ ├── 02.CountReadsRatio.py │ ├── 04.ConvertToGT.py │ ├── 06.MergeNonrecombinationRegion.py │ ├── 07.PlotHeatmap.py │ └── shell.sh └── 03.Sprime │ └── Sprime.py └── README.md /01.quality control/shell.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biozzq/goat-population-genetic/HEAD/01.quality control/shell.sh 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