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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
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choosing the right size for -b flad (breakpoint size) in cnvanator_to_bedpes.py #349

Closed nitinra closed 3 years ago

nitinra commented 3 years ago

Hello all,

I am trying to merge CNVnator calls to lumpy and using the cnvanator_to_bedpes.py to do it. However, to convert it, one needs the breakpoint size. How do I determine the correct size for the -b flag?

Thank you!

ryanlayer commented 3 years ago

What window size did you use for CNVnator?

On Wed, Dec 16, 2020 at 11:56 AM Nitin Ravikanthachari < notifications@github.com> wrote:

Hello all,

I am trying to merge CNVnator calls to lumpy and using the cnvanator_to_bedpes.py to do it. However, to convert it, one needs the breakpoint size. How do I determine the correct size for the -b flag?

Thank you!

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nitinra commented 3 years ago

What window size did you use for CNVnator? … On Wed, Dec 16, 2020 at 11:56 AM Nitin Ravikanthachari < @.***> wrote: Hello all, I am trying to merge CNVnator calls to lumpy and using the cnvanator_to_bedpes.py to do it. However, to convert it, one needs the breakpoint size. How do I determine the correct size for the -b flag? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#349>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEUGUMG6GEUBEUDOV3GEFDSVD7HJANCNFSM4U6OB4TA .

I used a bin size of 1000 (since my genomes had a coverage between 5-8x) while running CNVnator

ryanlayer commented 3 years ago

The breakpoint size allows you to adjust the precision of those calls. With 1000 bp windows I would suggest using 250 bp windows around the ends of the calls.

On Dec 16, 2020, at 6:05 PM, Nitin Ravikanthachari notifications@github.com wrote:

 What window size did you use for CNVnator? … On Wed, Dec 16, 2020 at 11:56 AM Nitin Ravikanthachari < @.***> wrote: Hello all, I am trying to merge CNVnator calls to lumpy and using the cnvanator_to_bedpes.py to do it. However, to convert it, one needs the breakpoint size. How do I determine the correct size for the -b flag? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#349>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEUGUMG6GEUBEUDOV3GEFDSVD7HJANCNFSM4U6OB4TA .

I used a bin size of 1000 (since my genomes had a coverage between 5-8x) while running CNVnator

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nitinra commented 3 years ago

thank you for your quick reply!

xiucz commented 3 years ago

how about the b size for the 5000bp window size cnvnator ? Thank you .

ryanlayer commented 3 years ago

1,250 seems reasonable.

On Wed, Apr 21, 2021 at 7:27 AM xiucz @.***> wrote:

how about the b size for the 5000bp window size cnvnator ? Thank you .

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