Closed JunpengShi closed 5 years ago
JunpengShi
commented
5 years ago Some followups, I just want to annotate the functional consequence of these structural variations. VCF format is the stadard file format for some variant predictors such as snpEff and VEP.
MariaNattestad
commented
5 years ago I’m not sure if there are any tools for that, so I think your best bet is to write a custom script like in python. Just note that VCF formats for structural variants are not well standardized, and the tools you mentioned may only be able to work with very specific formats.
Good luck!
On Sat, Jun 22, 2019 at 2:19 AM Junpeng Shi notifications@github.com wrote:
Some followups, I just want to annotate the functional consequence of these structural variations. VCF format is the stadard file format for some variant predictors such as snpEff and VEP.
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AG-Run
commented
3 years ago It would be nice if there is any script already to convert Assemblytics output to VCF, in order other tools can accept this output.
Thanks
mschatz
commented
3 years ago SURVIVOR has some support for this: https://github.com/fritzsedlazeck/SURVIVOR
Good luck!
Mike
On Wed, Nov 4, 2020 at 9:45 AM AGR notifications@github.com wrote:
It would be nice if there is any script already to convert Assemblytics output to VCF, in order other tools can accept this output.
Thanks
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AG-Run
commented
3 years ago Cordial greeting. Thanks for your answer, however Im not been able to get in the same VCF file all types of variants.
The command request "TYPE", thus, is there any way to put ALL types of variants, in order the vcf output extract all the variants identified by assemblytics.
In the moment if I type DEL, Survivor changes all the variants to Deletions even the insertions are marked as Deletions
thanks
El mié., 4 nov. 2020 a las 10:26, Michael Schatz (notifications@github.com) escribió:
SURVIVOR has some support for this: https://github.com/fritzsedlazeck/SURVIVOR
Good luck!
Mike
On Wed, Nov 4, 2020 at 9:45 AM AGR notifications@github.com wrote:
It would be nice if there is any script already to convert Assemblytics output to VCF, in order other tools can accept this output.
Thanks
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mschatz
commented
3 years ago Hmmm.... Can you fill a ticket with SURVIVOR to see if they can address?
On Wed, Nov 4, 2020 at 10:29 AM AGR notifications@github.com wrote:
Cordial greeting. Thanks for your answer, however Im not been able to get in the same VCF file all types of variants.
The command request "TYPE", thus, is there any way to put ALL types of variants, in order the vcf output extract all the variants identified by assemblytics.
In the moment if I type DEL, Survivor changes all the variants to Deletions even the insertions are marked as Deletions
thanks
El mié., 4 nov. 2020 a las 10:26, Michael Schatz (< notifications@github.com>) escribió:
SURVIVOR has some support for this: https://github.com/fritzsedlazeck/SURVIVOR
Good luck!
Mike
On Wed, Nov 4, 2020 at 9:45 AM AGR notifications@github.com wrote:
It would be nice if there is any script already to convert Assemblytics output to VCF, in order other tools can accept this output.
Thanks
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https://github.com/MariaNattestad/Assemblytics/issues/17#issuecomment-721773900
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-- Adriana María Gallego Rúa *Investigadora *Laboratorio de Biotecnología Universidad de Antioquia
ColombiaMedellín-2020
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AG-Run
commented
3 years ago I already did
Thanks
El mié., 4 nov. 2020 a las 10:42, Michael Schatz (notifications@github.com) escribió:
Hmmm.... Can you fill a ticket with SURVIVOR to see if they can address?
On Wed, Nov 4, 2020 at 10:29 AM AGR notifications@github.com wrote:
Cordial greeting. Thanks for your answer, however Im not been able to get in the same VCF file all types of variants.
The command request "TYPE", thus, is there any way to put ALL types of variants, in order the vcf output extract all the variants identified by assemblytics.
In the moment if I type DEL, Survivor changes all the variants to Deletions even the insertions are marked as Deletions
thanks
El mié., 4 nov. 2020 a las 10:26, Michael Schatz (< notifications@github.com>) escribió:
SURVIVOR has some support for this: https://github.com/fritzsedlazeck/SURVIVOR
Good luck!
Mike
On Wed, Nov 4, 2020 at 9:45 AM AGR notifications@github.com wrote:
It would be nice if there is any script already to convert Assemblytics output to VCF, in order other tools can accept this output.
Thanks
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <
https://github.com/MariaNattestad/Assemblytics/issues/17#issuecomment-721773900
, or unsubscribe <
https://github.com/notifications/unsubscribe-auth/AABP345MVJCD2DEDKYPRRTDSOFSH3ANCNFSM4H2WITRQ
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-- Adriana María Gallego Rúa *Investigadora *Laboratorio de Biotecnología Universidad de Antioquia
ColombiaMedellín-2020
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ColombiaMedellín-2020
Hi Nattestad, Do you have any recommended tools to convert Assemblytics bed output to vcf format?
Thanks, Junpeng