How to quickly tell the reference allele given chr, pos, A1 and A2 allele?
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!
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use samtools faidx ?
That is definitely a possible way. Thanks Pierre. But if ref allele is small indel, that could be a problem.
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.
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