User: EnsemblWill

gravatar for EnsemblWill
EnsemblWill560
Reputation:
560
Status:
Trusted
Location:
United Kingdom
Website:
http://www.ensembl.org...
Twitter:
EnsemblWill
Last seen:
1 year, 11 months ago
Joined:
4 years, 7 months ago
Email:
w**@ebi.ac.uk

Posts by EnsemblWill

<prev • 33 results • page 1 of 4 • next >
5
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Answer: A: VEP JSON output parsing
... VEP converts unbalanced substitutions (e.g. insertions, deletions) to an internal standard Ensembl representation. This is explained in basic terms [here][1]; essentially the leading base is trimmed from the REF and ALT alleles. However, this only explains what happens in the simple case, i.e. with ...
written 23 months ago by EnsemblWill560
3
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2
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2
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Answer: A: How to filter mutant allele frequency in Variant Effect Predictor (VEP)?
... VEP cannot do the filtering on the data as you have it. Typically frequency data is encoded in the INFO field of the VCF file, and VEP's accompanying filter script would allow you to filer on such a field. However, looking at the snippet you have pasted, VEP is unable to filter on this as it is not ...
written 2.0 years ago by EnsemblWill560
3
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2
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633
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2
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Answer: A: Why annotation doesn't respect VCF field schema ?
... The authors of VEP (myself) and snpEff collaborated on this format to a large extent. As far as we can tell it is the best way to cram in all of the annotation data provided by the tools to VCF. Your suggestion might be closer to the original intention of VCF spec, but it has a couple of flaws: - ...
written 2.4 years ago by EnsemblWill560
0
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1
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Answer: A: Using VEP: Variant Effect Predictor, how do I get the 1000G global Allele Freque
... > So, really, SAS_MAF was missing and all the numbers were misaligned This issue was noticed by a few users who had the version 85 GRCh37 VEP cache. AFAIK the issue is not present in the version 86 or 87 cache files, so if you are able to update then please use the newer version (you could also ...
written 2.5 years ago by EnsemblWill560
1
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1
answer
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1
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Answer: A: Plugin 'dbNSFP' of VEP went wrong
... Resolved on GitHub, please don't cross-post across help forums if you can avoid it! https://github.com/Ensembl/VEP_plugins/issues/29 ...
written 2.8 years ago by EnsemblWill560
2
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2
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Comment: C: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
... You'll need to unpack the gzipped FASTA file with $ gzip -d vep/v75/homo_sapiens/75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz Ensembl annotation on GRCh37 was frozen at release 75; while newer software releases still support using GRCh37, most data is frozen at 75, hence why the v75 FA ...
written 3.0 years ago by EnsemblWill560 • updated 3.0 years ago by genomax68k
3
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2
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Answer: A: VEP failed to parse TBX_GENERIC error
... The offending line reported is the header line from the dbNSFP data file. If it continues to run (and you get the expected data back from dbNSFP) then you can probably ignore it. If it's an error that persists and/or causes VEP to crash, try re-downloading and re-indexing the dbNSFP file according ...
written 3.7 years ago by EnsemblWill560
0
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1
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1.9k
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1
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Comment: C: Ensembl Perl API - How to get genotype frequencies
... The method links on this page: http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PopulationGenotype.html tell you what to expect to be returned from each method call. For example, the genotype method has the following info: Description: Getter for the ...
written 3.8 years ago by EnsemblWill560
3
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1
answer
1.9k
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1
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Answer: A: Ensembl Perl API - How to get genotype frequencies
... The method you're looking for is $variation->get_all_PopulationGenotypes(); http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Variation.html#a9e851dc76e253575f564d149b977c98e http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1 ...
written 3.8 years ago by EnsemblWill560
1
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1
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1.3k
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1
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Answer: A: Ensembl variant effect predictor bigWigToWig
... bigWigToWig is part of the UCSC kent source tree See this page for installation instructions: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source ...
written 4.0 years ago by EnsemblWill560

Latest awards to EnsemblWill

Scholar 23 months ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Scholar 2.0 years ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Scholar 3.8 years ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Scholar 4.1 years ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Scholar 4.2 years ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Scholar 4.3 years ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Scholar 4.3 years ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Appreciated 4.6 years ago, created a post with more than 5 votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Scholar 4.6 years ago, created an answer that has been accepted. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Ensembl VEP filtering most_severe keeping Symbol, Feature,Consequence etc.

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