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Align plink to fasta

Hello, I have genotyping data converted to plink files (binary files) that I want to merge. Before merging, I would like to align it to an human genome reference (that I have in fasta format) to avoid problems arising from incompatibility. Is it possible?

plink alignment fasta
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updated by Istvan Albert Istvan Albert • written by 818fd56e • 818fd56e

What do you mean by 'align'? Make sure the reference and alternate alleles are the same?

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written by 4galaxy77 4galaxy77

1 answer

The plink file contains variants; you can't "align" those against any reference.

If you mean you want to validate that the variants were produced from a specific reference, then you could do so by converting your binary files to VCF files and then applying a variant normalization

For example, recode the plink file into VCF, then use bcftools norm to normalize the resulting variants.

Other validation methods may also exist.

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written by Istvan Albert Istvan Albert

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