Hi, I converted the vcf file into hapmap file using plink. Then compare the alleles between genotypes using awk commands like following:
rs# alleles chrom pos strand genotypeA genotypeB
S01_9567 A/C 01 9567 + A N Different
S01_9737 T/C 01 9737 + N N Same
S01_9776 T/C 01 9776 + T N Different
S01_9903 T/C 01 9903 + Y T Different
S01_10418 G/A 01 10418 + G N Different
S01_10770 A/T 01 10770 + A A Same
S01_10818 G/C 01 10818 + G G Same
S01_10837 C/T 01 10837 + Y Y Same
S01_10908 G/A 01 10908 + G G Same
S01_10921 G/A 01 10921 + R R Same
is this fine? Looking forward your valuable comments?
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rj.rezwan •
Most probably you can use the approach explained here in
Plink. Are you wanting to compare alleles of two or more genotypes or compare pairwise linkage disequilibrium between SNPs? Please clarify further.Actually, I have 3 accessions having the same names. But at the vegetative stage, they have morphological differences. That's the reason I want to check them to see where they have the allele difference. This was the main reason, I put the question here. If you have some more suggestions about this, I will be grateful.