Open mixle18 opened 10 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
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