search

BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
142 stars 41 forks source link

Haplotype blocks from whole chromosome #36

Open mixle18 opened 11 months ago

mixle18 commented 11 months ago

Hi, I am working on the plant genome and I am interested in finding the haplotype blocks in my whole chromosome. Is it okay, if I put the coordinates of whole chromosomes for finding the haplotype blocks and then visualize the specific blocks?

Also, I am curious about how to define the haplotype blocks in the output.

Thank you in advance Megha Sharma

hewm2008 commented 11 months ago

hi Megha Sharma: For all chromosomes to find haplotype blocks . you can try by the other tools ,plink with --blocks no-pheno-req (plink you can find it in LDBlockShow/bin/plink ) 

./LDBlockShow*/bin/plink     --vcf     in.vcf      --snps-only   --geno  0.25     -maf    0.05     -hwe    0     --blocks   no-pheno-req  --allow-extra-chr   --out         plink.block.out