rtracklayer: how to view coordinates that failed liftover?
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chang02_23 ▴ 30
@chang02_23-7435
Last seen 6.0 years ago
United States

I am ilfting over SNV calls from hg38 to hg19 using rtracklayer. The liftover result has less number of lines that my input. How do i figure out which SNV calls failed liftover?

 

rtracklayer • 991 views
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@michael-lawrence-3846
Last seen 2.4 years ago
United States

liftOver() yields a GRangesList, with one element per input range. I'm not sure what you mean by "lines" but I guess you are unlisting the result and writing it to a file. Instead of unlisting, you can just look at the lengths() of the return value to determine the degree of mapping for each input range.

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Aha! I unlist the result so I couldn't figure out how to map each input range. Thank you.

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