User: LGMgeo

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LGMgeo90
Reputation:
90
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Trusted
Location:
European Union
Last seen:
7 months, 2 weeks ago
Joined:
5 years, 8 months ago
Email:
v*****************@inserm.fr

Posts by LGMgeo

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Annotation for SV and CNV
... Yes, you just need an SV input file in a VCF or BED format. ...
written 7 months ago by LGMgeo90
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Answer: A: Annotation of Pindel files using AnnotSV
... Hi, A bugfix has been added in AnnotSV, this SV length bad report should no longer be encountered. It's better to directly send an email to the author (me) for any bug that you can detect. Otherwise, it is to notice that the AnnotSV output is a tsv file (tabulated separated values), not a VCF one. ...
written 7 months ago by LGMgeo90
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Comment: C: 1000Genome SV integrated map's power for SV filter
... For 2 days, we experienced some technical problems with our network, so that you can not access the AnnotSV website. I apologize for any inconvenience that may be caused by this temporary interruption. ...
written 19 months ago by LGMgeo90
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Answer: A: Using AnnotSV to annotate XHMM output
... ANNOTSV is the environment variable defining the installation path of the software. • In csh, you can define it with the following command line: setenv ANNOTSV /path_of_AnnotSV_installation • In bash, you can define it with the following command line: Export ANNOTSV=/path_of_AnnotSV_installation ...
written 19 months ago by LGMgeo90
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Comment: C: Annotation for SV and CNV
... Could you please explain more? Can you give an input/output example of what you wish? ...
written 21 months ago by LGMgeo90
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Answer: A: annotation of SV (Structural Variants)
... I suggest using AnnotSV for SV annotation (annotation with gene names and locations, OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information). AnnotSV constructs an annotation based on the full-length SV but also an annotation for each gene within the SV. You will ...
written 2.0 years ago by LGMgeo90
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Comment: C: annotation of SV (structural variants)
... I suggest using AnnotSV for SV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information) You can look at this post describing the annotSV tool: https://www.biostars.org/p/196944/ ...
written 2.0 years ago by LGMgeo90
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Comment: C: Methods of classifying, not detecting, structural variation?
... - To identify how similar a structural variant (SV) is to a known variant from DGV, 1000g or DECIPHER, I suggest using AnnotSV. You can look at this post describing the annotSV tool: https://www.biostars.org/p/196944/ - Else, if you want to identify similar SV detected from different callers, I ad ...
written 2.0 years ago by LGMgeo90
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Comment: C: Is there any suitable annotation tool for structural rearrangements?
... I suggest using AnnotSV for SV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information) You can look at this post describing the annotSV tool: https://www.biostars.org/p/196944/ ...
written 2.0 years ago by LGMgeo90
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Comment: C: How Can I Annotate Cnvs
... I suggest using AnnotSV for CNV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information) . You can look at this post describing the annotSV tool: https://www.biostars.org/p/196944/ ...
written 2.0 years ago by LGMgeo90

Latest awards to LGMgeo

Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Annotation for SV and CNV
Popular Question 2.3 years ago, created a question with more than 1,000 views. For TAD (Topologically Associating Domain) boundaries
Student 2.8 years ago, asked a question with at least 3 up-votes. For TAD (Topologically Associating Domain) boundaries

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