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BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
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-NoLogP not working #16

Closed huw143 closed 3 years ago

huw143 commented 3 years ago

Hello,

Could you help me solve the "-NoLogP" code by any chance? it looks not working.

for example,

../bin/LDBlockShow -InVCF GWAS_Only_Chromosome_Biallelic.Filter_out.0.05MAF_50%Missing.vcf.gz -MAF 0.05 -Miss 0.6 -OutPut Chr2.4_58225679 -Region chr2.4:54758224-59306183 -SpeSNPName Chr2.4_58225679_spe.snp -InGWAS Chr2.4_58225679_gwas.pvalue -Cutline 5 -OutPng -SeleVar 1 -ShowNum -BlockType 3 -BlockCut 0.8 -NoLogP

I was trying to put -NoLogP at different positions, it still did not work.

Any help would be appreciated!

Hu

hewm2008 commented 3 years ago

@huw143
-NoLogP is the Para for the replot bin [ShowLDSVG] ,no for the LDBlockShow . after LDBlockShow , you can replot by follow :

LDBlockShow-1.40/bin/ShowLDSVG -InPreFix Chr2.4_58225679 -SpeSNPName Chr2.4_58225679_spe.snp -InGWAS Chr2.4_58225679_gwas.pvalue -Cutline 5 -OutPng -ShowNum -BlockCut 0.8 -NoLogP

LDBlockShow-1.40/bin/ShowLDSVG LDBlockShow-1.40/bin/ShowLDSVG -help LDBlockShow-1.40/bin/ShowLDSVG -MoreHelp