allele matching between identical genotypes

Question

[rj.rezwan]

Hi, I have the variant calling output in the form of vcf files. Variant calling was done with GATK haplotypecaller. I am interested in performing the allele matching between two identical genotypes. So what is the best way to perform this or which tool can do this best? Please suggest

[bk11]

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.

[rj.rezwan]

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.

Answer 1

[chrchang523]

Plink 2.0's --sample-diff command provides one way to list differences between two samples.

Since there are only a few samples, it is also practical to do this with an awk one-liner operating on the VCF.

[rj.rezwan]

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?