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VEP: Generation of polyphen2 & SFT scores for structural variants.
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DBD::mysql required for VEP installation?
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VEP [E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip
written by Filago 11Hello! I installed VEP with the INSTALL.pl script without any error, but when running it the following error occurs: [E::fai_build3_core] Cannot index files compressed with …
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Get REVEL plugin started with VEP
written by Filago 11Hello, I am using the VEP tool (version 104) and already managed to annotate a VCF-file (hg19) with basic annotations and CADD. Furthermore I wanted …
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How to find genomic coordinates of the HumVar and HumDiv datasets
written by Eric Wang 7Hello all, I am looking for the list of genomic coordinates and variants for the HumVar and HumDiv datasets. Is there any way to obtain …
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HumVar and HumDiv genomic coordinates
written by mathieu.quinodoz 0Hello all, I am looking for the list of genomic coordinates and variants for the HumVar and HumDiv datasets (like a vcf file). From the …
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PolyPhen Humdiv vs HumVar discrepancies
written by cocchi.e89 30Dear all, as far as I know Polyphen2 (http://genetics.bwh.harvard.edu/pph2/) predicts variant effect based on 2 different DB: - **HumDiv**: *Mendelian disease variants vs. divergence from …
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VEP and Annovar Annotation
written by BAGeno 19Hi, I am trying to figure out which tool VEP or Annovar, is most accurate in terms of SIFT and Polyphen annotation. I annotated my …
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VEP vs webserver Polyphen scores
written by regrant 2Hello, I have recently noted a discrepancy the scores given by running PolyPhen at its [website][1] vs getting the PolyPhen score from ensembl's variant effect …
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Polyphen-2 Classifier Model
written by learnerforever 52<p>On the polyphen-2 webpage</p> <p><a href="http://genetics.bwh.harvard.edu/pph2/bgi.shtml">http://genetics.bwh.harvard.edu/pph2/bgi.shtml</a></p> <p>There are two options for the classifier model:</p> <p>HumDiv HumVar</p> <p>Could anyone explain what these are? Is there a …