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Strand for GTEx WGS data?

Hello!

I'm working with GTEx v8 WGS data for the first time, and I'm having trouble finding strand information for the variants in their genotype calls. There doesn't seem to be any strand information given in the WGS file itself, which makes me think that they're all mapped to the same strand (presumably +). However, I haven't found any confirmation of this on the GTEx web site or the readme files included with the data.

Can anyone confirm that the variants reported in GTEx data are all from a particular strand? Or can anyone point me to where strand information for variants in the v8 WGS data is reported?

Thank you!

gtex wgs strand
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written by spitzer • spitzer

1 answer

WGS is not a strand-specific assay neither is the concept of a DNA variant, unlike genes and/or coding sequences. DNA is double-stranded, therefore any variant on the plus strand also occurs on the bottom strand.

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written by ATpoint ATpoint

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