Insertion detection

[Madelinehazel]

Is Lumpy unable to detect insertions?

Thanks

[ryanlayer]

Yes and no. Large intra/inter-chromosomal insertions will be found and marked as BND. Large novel insertions will lead to unmapped reads, which lumpy cannot interpret. Small insertions are not supported.

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On Tue, Jan 10, 2017 at 1:51 PM, Madeline Couse ***@***.***> wrote: Is Lumpy unable to detect insertions? Thanks — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#160>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAlDUVLgicrpneFjLFdGeDUJudD44_1vks5rQ-9egaJpZM4Lf4Vf> .

-- Ryan Layer

[Madelinehazel]

Thanks. Is there any kind of post-processing that can be done to determine which BND are insertions?

[ryanlayer]

You can go back and look for both side of the insertion.

[ryanlayer]

A true insertion will have 2 BND, you can start by looking for those.

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On Wed, Jan 18, 2017 at 12:40 PM, Madeline Couse ***@***.***> wrote: Thanks. Is there any kind of post-processing that can be done to determine which BND are insertions? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#160 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAlDUQ3JSE3RsewY5nUOKorlhXwYn6LQks5rTmrIgaJpZM4Lf4Vf> .

-- Ryan Layer