Difference between revisions of "2017 Nov Taeyoung Lab note"

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(Created page with "== 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...")
 
 
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== LD using Hapview ==
 
== 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
 
  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
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== selective sweep ==
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1. fst
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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
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2. pi
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vcftools --vcf variant.SG.vcf.without.vege.maf0.01.recode.vcf.SNP.d3.m0.2.vcf --window-pi 100000 --window-pi-step 20000
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3. fst filtering
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python get_fst_95tail.py
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4. Pic/Pil
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python get_PIcPIl.py
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5. get overlap
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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
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6. make block by manual
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7. ret gene on selective sweep block
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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

Latest revision as of 01:07, 30 November 2017

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