2017 Nov Taeyoung Lab note
From Crop Genomics Lab.
LD using Hapview
java -jar /alima9002/program/Haploview/Haploview.jar -nogui -out variant.SG.vcf.SNP.Q30.d5.hapview.out.rsq.%s -dprime -svg -compressedpng -minMAF 0.01 -memory 1024 -haps %s -info %s.info -ldvalues NONE -ldcolorscheme RSQ -maxDistance 1000
selective sweep
1. fst
vcftools --vcf variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf --weir-fst-pop SG_Landrace.bamlist --weir-fst-pop SG_Cultivar.bamlist --fst-window-size 10000 --fst-window-step 2000 --out variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.10k
2. pi
vcftools --vcf variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf --window-pi 100000 --window-pi-step 20000
3. fst filtering
python get_fst_95tail.py
4. Pic/Pil
python get_PIcPIl.py
5. get overlap
python get_overlap_fstNrod.py variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.100k.windowed.weir.fst.significant variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.100k.ROD.significant > variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf.selective.sweep.in.100k.by.fstNrod
6. make block by manual
7. ret gene on selective sweep block
python get_gene_from_selective_sweep.py selective_sweep_block_in_100k.txt /alima9002/ref/Gmax/annotation/Gmax_275_Wm82.a2.v1.gene.gff3 > selective_sweep_block_in_100k.txt.gene