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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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Overlapping SNP name #14

Closed huw143 closed 3 years ago

huw143 commented 3 years ago

Hi,

Do you know how to solve the overlapping SNP names in the plot? or How to stop the software to skip the high missing sites, why it is always skipping the highly missing sites, I already filter out the 50% missing genotypes and 5% MAF from my VCF file? (I believe this is the reason why SNP names are overlapping)

Please see the attachment

Thank you very much,

Hu Chr4 1_68942611

hewm2008 commented 3 years ago

1 For high missing sites ,you can change the defaut value of para [-Miss ] and the [ -MAF ] . LDBlockShow-1.40/bin/LDBlockShow -h you will see the filter para :

                -MAF           <float>    Min minor allele frequency filter [0.05]
                -Miss          <float>    Max ratio of miss allele filter [0.25]
                -HWE           <float>    Exact test of Hardy-Weinberg Equilibrium for SNP Pvalue[0]
                -Het           <float>    Max ratio of het allele filter [1.00]

-Miss 0.5

2 For [SNP names are overlapping] I think it's the data in you input [ -SpeSNPName SpeSNPName.file], you should filter same sites which is no in the XXX.site.gz

3 If you can read Chinese and have QQ chat , you can join the QQ group【125293663】 and contact me(hewm2008)