├── Admixtue ├── admixture.R ├── admixture.sh └── script.sh ├── CNVindex ├── CNVindexScan.R └── script.sh ├── Demography ├── 2epoch.py ├── 2epoch_m.py ├── 3epoch.py ├── 3epoch_m.py ├── 3epoch_m1.py ├── 3epoch_m2.py ├── 3epoch_m_single.py ├── 3epoch_m_single2.py ├── 4DTv.py ├── esti_theta_from_sfs.py └── script.sh ├── Fst ├── script_DE_vs_DO.sh └── script_HA_vs_LA.sh ├── GWAS └── script.sh ├── LICENSE ├── NJ_tree └── NJtree_iTOL.R ├── PAV └── script.sh ├── PCA ├── plot.R └── script.sh ├── README.md ├── Zang1817_assembly ├── 1.find_position.sh ├── 2.anchor.sh ├── FastaOrderByList.cpp ├── GenerateReads_WG_PE.cpp ├── REAME ├── ThreadFasta.cpp └── demo_data │ ├── IWGSCv1.fa │ └── Zang1817.fa ├── pi-ratio └── script.sh └── variant_calling ├── 01.split ├── 01.Split.sh ├── Split.sh └── Split_local.sh ├── 02.trimmomatic ├── 02.trimmomatic.sh ├── trimmomatic.sh └── trimmomatic_local.sh ├── 03.bwa ├── 03.bwa.sh ├── bam_stat.sh └── bwa.sh ├── 04.filter ├── 04.filter.sh ├── filter.list └── filter.sh ├── 05.mergeAsplit ├── 05.mergeAsplit.sh └── mergeAsplit.sh ├── 06.callsnp ├── 06.callsnp.sh ├── checkFinish.sh ├── csp.sh ├── justcall.sh ├── justcall_script.sh └── justuniq.sh ├── 07.splitGVCF ├── 07.splitGvcf.sh ├── SplitGvcfByBin.py ├── break.ref └── splitScript.sh ├── 08.mergeGVCF ├── 08.mergeGvcf.sh └── 08.merge_script_two_parts.sh ├── 09.filterVCF ├── 09.filterAmerge.sh └── VCFfilter.sh └── 10.concatVCF ├── 10.concat.sh ├── concatVCF.sh └── header_length.txt /Admixtue/admixture.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wangzihell/CAU-TibetanWheatSeq/HEAD/Admixtue/admixture.R -------------------------------------------------------------------------------- /Admixtue/admixture.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wangzihell/CAU-TibetanWheatSeq/HEAD/Admixtue/admixture.sh 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