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Trinotate / Trinotate.github.io

web documentation for Trinotate
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How to annotate SNPs #18

Open ShuChen1986 opened 5 years ago

ShuChen1986 commented 5 years ago

Hi, After we called variants using the GATK pipeline, is there a way to annotate the variants as synonymous or non-synonymous using ORF annotations generated by Transdecoder? Thank you so much! Shu

brianjohnhaas commented 5 years ago

Hi Shu,

I haven't added code or documentation to do this, but I do know that it's possible based on others experiences. Try looking into snpEff and see if that'll meet your variant annotation needs.

best,

~brian

On Mon, Apr 29, 2019 at 4:50 AM ShuChen1986 notifications@github.com wrote:

Hi, After we called variants using the GATK pipeline, is there a way to annotate the variants as synonymous or non-synonymous using ORF annotations generated by Transdecoder? Thank you so much! Shu

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/18, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZRKX4D7PZ7MUWVM35HNYDPS2ZEDANCNFSM4HJBNK7Q .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

ShuChen1986 commented 5 years ago

Hi Shu, I haven't added code or documentation to do this, but I do know that it's possible based on others experiences. Try looking into snpEff and see if that'll meet your variant annotation needs. best, ~brian … On Mon, Apr 29, 2019 at 4:50 AM ShuChen1986 @.***> wrote: Hi, After we called variants using the GATK pipeline, is there a way to annotate the variants as synonymous or non-synonymous using ORF annotations generated by Transdecoder? Thank you so much! Shu — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18>, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZRKX4D7PZ7MUWVM35HNYDPS2ZEDANCNFSM4HJBNK7Q . -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

Hi, Brian, Thank you so much for your reply. But the snpEff is used in analysis with a reference genome. I have tried to use kissplice but the result is not good enough. I will try to optimize the setting for kissplice. See how it goes! Thank you! Shu

brianjohnhaas commented 5 years ago

I think there should be a way to run snpeff using the Trinity supertranscripts as the reference. Once upon a time, someone sent me some info on this. I'll try to locate it and make it more broadly available.

On Tue, Apr 30, 2019 at 3:40 AM ShuChen1986 notifications@github.com wrote:

Hi Shu, I haven't added code or documentation to do this, but I do know that it's possible based on others experiences. Try looking into snpEff and see if that'll meet your variant annotation needs. best, ~brian … <#m-2398037837183472021> On Mon, Apr 29, 2019 at 4:50 AM ShuChen1986 @.***> wrote: Hi, After we called variants using the GATK pipeline, is there a way to annotate the variants as synonymous or non-synonymous using ORF annotations generated by Transdecoder? Thank you so much! Shu — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18 https://github.com/Trinotate/Trinotate.github.io/issues/18>, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZRKX4D7PZ7MUWVM35HNYDPS2ZEDANCNFSM4HJBNK7Q . -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

Hi, Brian, Thank you so much for your reply. But the snpEff is used in analysis with a reference genome. I have tried to use kissplice but the result is not good enough. I will try to optimize the setting for kissplice. See how it goes! Thank you! Shu

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/18#issuecomment-487849179, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZRKX2OLSXFGKC7E3LUOHDPS7ZXVANCNFSM4HJBNK7Q .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

brianjohnhaas commented 5 years ago

Hi,

Paul Maier had shared his protocol with me to do this, and he's allowing me to make it publicly available via our trinity community codebase. I put it all here for now: https://github.com/trinityrnaseq/trinity_community_codebase/tree/master/annotating_snps

Let's see if that helps.

best,

~brian

On Tue, Apr 30, 2019 at 8:54 AM Brian Haas bhaas@broadinstitute.org wrote:

I think there should be a way to run snpeff using the Trinity supertranscripts as the reference. Once upon a time, someone sent me some info on this. I'll try to locate it and make it more broadly available.

On Tue, Apr 30, 2019 at 3:40 AM ShuChen1986 notifications@github.com wrote:

Hi Shu, I haven't added code or documentation to do this, but I do know that it's possible based on others experiences. Try looking into snpEff and see if that'll meet your variant annotation needs. best, ~brian … <#m_9010847784816281240m-2398037837183472021_> On Mon, Apr 29, 2019 at 4:50 AM ShuChen1986 @.***> wrote: Hi, After we called variants using the GATK pipeline, is there a way to annotate the variants as synonymous or non-synonymous using ORF annotations generated by Transdecoder? Thank you so much! Shu — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18 https://github.com/Trinotate/Trinotate.github.io/issues/18>, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZRKX4D7PZ7MUWVM35HNYDPS2ZEDANCNFSM4HJBNK7Q . -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

Hi, Brian, Thank you so much for your reply. But the snpEff is used in analysis with a reference genome. I have tried to use kissplice but the result is not good enough. I will try to optimize the setting for kissplice. See how it goes! Thank you! Shu

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/18#issuecomment-487849179, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZRKX2OLSXFGKC7E3LUOHDPS7ZXVANCNFSM4HJBNK7Q .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas