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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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How can I close the quality check on my data? #25

Closed janking1 closed 8 months ago

janking1 commented 2 years ago

Hi there, I have two genotype data in PLINK format with the same BIM file and different FAM file, now I tried to compare the LD in two dataset without quality check, how can I do that in LDBlockShow?

hewm2008 commented 2 years ago

you can run LDblockShow with these two datas separately, you will get two graphs, then you can compare the difference between the two graphs

janking1 commented 2 years ago

you can run LDblockShow with these two datas separately, you will get two graphs, then you can compare the difference between the two graphs

Maybe my question wasn't described clear enough. My problem is I did draw two graphs separately, but these two graphs didn't have the same start bp and end bp because of the auto data check in LDblockShow and now I want to close it so I can draw two graphs without quality check and compare them in the same total SNP .

hewm2008 commented 2 years ago

Indel and no bi-allelic SNP will must be filter,only bi-allelic SNP will be take in . The other filter para（maf miss hete ）, you can set it to be a extreme values ​​make it unfiltered. I suggest you can try

   LDBlockShow-1.40/bin/LDBlockShow   -MAF    0.0001   -Miss    1.0   -HWE    0  -Het   1.0  ...
 
    -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]