Liftover using gVCF
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Entering edit mode
2.5 years ago

Hi,

I recently acquired a large dataset. Unfornetly, the new dataset that I acquired uses a human genome 19 while my original dataset uses human genome 38. Both datasets have gVCFs so what I was wondering is, is it possible to using liftover on a gVCF? I saw some post from almost 10 years ago referencing Gvf, however, I was hoping to find more recent information about this topic. What was provided from the new dataset was only the gVCFs and VCF files for each sample. No data was provided that would allow me to realign the data to a different genome. Even if there was, both datasets are so large that this would quickly turn into a massive project.

My goal here, at least what I was hoping to do, is to perform joint genotyping on all the samples from both datasets. I figured performing liftover on the gVCF would allow me to do joint genotyping on both data sets.

genome assembly GATK liftover • 816 views
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Entering edit mode
2.5 years ago
Sam ★ 4.7k

Think CrossMap natively support gVCF file: http://crossmap.sourceforge.net/#user-input-file

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