Checking chromosome builds for genotyping data
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8 months ago

Hi,

I have several studies worth of data (In both PLINK and vcf format), and I was wondering if anyone knew of an online tool which I could use to check my chromosome build i.e GRCh37 vs GRCh38. (I thought I used one before but I am since unable to find it).

Or if there are any other suggestions for how to best check this. I guess I could try merging study data with the reference builds and see what aligns best, but this will probably take a while to go through.

Thanks for any help,

Mari

GWAS Liftover PLINK • 298 views
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Entering edit mode
3 months ago
Vincent Laufer ★ 2.1k

While this should be known to the analyst going in, for a lot of reasons it isn't always ... there are more and less rigorous ways of determining this, but the simplest way I can think of is pick one marker per chromosome, and find which build matches the chr:position in every case ... after only a few you'll know the answer.

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