How to quickly tell the reference allele given chr, pos, A1 and A2 allele?

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3.9 years ago

Tao ▴ 530

Given the chromosome, position and A1 allele, A2 allele, how to easily tell which allele is the reference allele?

I know it is possible to extract the annotation from dbSNP, 1000G or other reference panels. But, that will need to download large mount of data. What I am looking are more efficient ways, such as online tools, command lines etc..

Thanks!

snp reference allele ref allele • 2.3k views

ADD COMMENT • link 3.9 years ago by Tao ▴ 530

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use samtools faidx ?

ADD REPLY • link 3.9 years ago by Pierre Lindenbaum 161k

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That is definitely a possible way. Thanks Pierre. But if ref allele is small indel, that could be a problem.

ADD REPLY • link 3.9 years ago by Tao ▴ 530

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How are you defining reference here? The one with the highest AF? The reference/alt allele for a given sample isn't necessarily in the reference genome.

ADD REPLY • link 3.9 years ago by benformatics 3.9k

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Hi, I think reference allele refers to the allele shown in the reference genome, isn't it? Please check the website: https://www.ebi.ac.uk/training/online/course/human-genetic-variation-i-introduction-2019/what-genetic-variation/what-are-variants-alleles

ADD REPLY • link 3.9 years ago by Tao ▴ 530

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