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Excavator - Error in JointSegIn

Hi.

I ran EXCAVATOR that detects copy number variations.

but, I was encountering some errors and I couldn't solve it.

excavator cnv
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updated by Ram Ram • written by mangfu100 mangfu100

Hi, I changed the title of your question to be more specific.

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Hi,

could you found how to resolve this issue ?

I have the same problem.

Thanks

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updated by Ram Ram • written by jp.of.mars • jp.of.mars

1 answer

Hi,

It's an old post, but I found it with google. On this post, Alberto recommend to remove overlapping coordinate in bed: https://sourceforge.net/p/excavator2tool/tickets/1/

So I ran:

sort -k1,1 -k2,2n mybedfile.bed | bedtools merge > mybedfile_merged.bed
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written by alexandre.atkinson • alexandre.atkinson

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