Question

What are reference alleles and alternate alleles in VCF (Variant Call Format) file?

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4.3 years ago

Tina ▴ 10

What are reference alleles and alternate alleles in VCF (Variant Call Format) file? Does reference allele mean the allele in the reference genome and alternate alleles are alleles we see in the patient we are studying?

SNP genome • 1.5k views

ADD COMMENT • link updated 4.3 years ago by Kevin Blighe 87k • written 4.3 years ago by Tina ▴ 10

score 1 · Answer 1 · 2020-01-05

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4.3 years ago

Kevin Blighe 87k

Yes, but be aware of these situations: A: Minor Reference Allele Frequency in GRCh37/hg19

Kevin

ADD COMMENT • link 4.3 years ago by Kevin Blighe 87k