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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Does lumpy double count the support at a particular location? #297

Open MarkDunne opened 5 years ago

MarkDunne commented 5 years ago

Hi,

Suppose I have a translocation from site A to site B. In the VCF entry at site A, will lumpy give me the number of split reads (or paired end reads) that support that variant at site A only, or does it include support from the reads at site B?

Thanks

ryanlayer commented 5 years ago

Yes, but you need to go search for B.

On Tue, Mar 5, 2019 at 11:35 AM Mark Dunne notifications@github.com wrote:

Hi,

Suppose I have a translocation from site A to site B. In the VCF entry at site A, will lumpy give me the number of split reads (or paired end reads) that support that variant at site A, or does it include support from the reads at site B?

Thanks

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MarkDunne commented 5 years ago

Thanks Ryan. What you're referring to is finding the mate in the VCF I presume?

So if the counting is done this way, and we were trying to calculate the number of reads containing a SV in a particular location, would it be correct to take the split read support + paired end read support and divide that by 2?