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concordance errors

wangj27wangj27 new york cityMember

Hi, I met a problem when I try to use genotype concordance to compare one trio tested on 2 different platform. One is Agilent, the other is Nimblegene. I want to compare the concondance of each family members in the 2 platforms. I got the following:"1305446EX.combined.vcf and reference have incompatible contigs: No overlapping contigs found" I am use hg19.fasta as reference

I guess my method using concondance might be not 100% correct or something I misunderstood. Could you guide me how to compare them?

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