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Concordance due to difference in genotype

h_asifh_asif Member
edited July 2015 in Ask the GATK team

hi there
i use Selectvariant to find common SNPs b/w two files is there any way i can find concordance b/w two files based on differences in genotype
SNP A position 123 is present in both file 1 and 2 but in file 1 it is HOMO and in file 2 its hetero
i use Select variants it give me what i want but it was giving me all common SNPs with same and different genotype
while i am interested in those common snps that have different genotype


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