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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Can I get the copy number information? #375

Closed hayeon-pak closed 2 years ago

hayeon-pak commented 2 years ago

Hello,

I am trying to CNV analysis and going to make CNV plots. So, I used lumpy and was able to get result of DEL, DUP, INV and etc using lumpyexpress and svtyper. But I can't find copy number of DEL and DUP. Can I get the copy number only from the result? or which column is this?

Thank you.

ryanlayer commented 2 years ago

For DEL the copy number is reflected in the genotype 0/1 is one copy loss and 1/1 is two copy loss. For DUP, we do something similar, but it is not as straightforward. I would suggest running CNVnator on your samples to estimate copy number.

On Mon, Feb 14, 2022 at 11:06 PM hayeon-pak @.***> wrote:

Hello,

I am trying to CNV analysis and going to make CNV plots. So, I used lumpy and was able to get result of DEL, DUP and INV... using lumpyexpress and svtyper. But I can't find copy number of DEL and DUP. Can I get the copy number only from the result? or which column is this?

Thank you.

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hayeon-pak commented 2 years ago

Thank you for reply :) I will refer to your answer.