User: rbagnall

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rbagnall1.2k
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Posts by rbagnall

<prev • 96 results • page 1 of 10 • next >
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Answer: A: Find Intersections Between ClinVar Track and VCF In IGV
... You can download clinvar as a vcf, aligned to GRCh37 or GRCh38 from [here][1] The vcf INFO column contains the clinvar allele id (ALLELEID) and clinical significance, e.g. CLNSIG=Benign, CLNSIG=Pathogenic, so you could load both in IGV, or compare your vcf with the clinvar vcf for similar alleles u ...
written 9 days ago by rbagnall1.2k
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Comment: C: Update RefSeq database with Ensembl VEP
... Thanks Emily, that worked! For those that are interested, I got the gff file from here: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gff.gz Then unzipped, sorted, bgzipped and tabix indexed, as described on the VEP link provided ...
written 6 weeks ago by rbagnall1.2k
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Update RefSeq database with Ensembl VEP
... Hi, I'm using the most current version of VEP (Ensembl variant effect predictor v92.3) and annotating against the RefSeq transcripts. The output shows that it is using `refseq version 01_2015` How can I update this to a more recent release? I can't seem to find where the refseq database has bee ...
ensembl vep refseq written 6 weeks ago by rbagnall1.2k • updated 6 weeks ago by Emily_Ensembl15k
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Comment: C: How can I deal with this publication issue?
... Not really the right place for this question. It's best to sort this out way before submission. When you submitted the review, who did you list as authors, and which institution did you list as your affiliation? ...
written 11 weeks ago by rbagnall1.2k
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Answer: A: gnomad_AF from VEP is NA
... It may depend on the ethnicity of the sample(s). An Australian Indigenous person will show many apparently novel variants, although most will be ethnic specific and this population is not represented in GnomAD. In this case, the variants are absent from GnomAD, but not necessarily 'rare' in the Aust ...
written 3 months ago by rbagnall1.2k
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Comment: C: snpEff inappropriate interpretation of variants?
... Yeah, possibly. It may be a default annotation of an important amino acid residue. ...
written 11 months ago by rbagnall1.2k
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Answer: A: snpEff inappropriate interpretation of variants?
... In the second example, the ensEMBL transcript ENST00000575124 has a protein coding region that extends into the intronic regions of other transcripts of this gene, and so explains the frameshift. You can see the extended protein coding region of transcript ENST00000575124 in the [UCSC genome browser ...
written 11 months ago by rbagnall1.2k
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Answer: A: Which tool to calculate per site stats on vcf file?
... bcftools with the [fill-tags][1] plugin will add this info to the vcf file. [1]: https://samtools.github.io/bcftools/howtos/plugin.fill-tags.html ...
written 11 months ago by rbagnall1.2k
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Answer: A: Extracting Codons from a SNP alignment
... The web-based too [SIFT/Provean][1] will do this for you. Given a list of input variants in the form of: chromosome,position,reference allele,alternate allele: 1,100382265,C,G it will return: TCC [C/G]GA CAT (amongst other things) where your variant codon is in the middle and the flanking co ...
written 12 months ago by rbagnall1.2k
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Answer: A: CNVnator error :Can't determine length for 'chr1'. No reference genome specified
... CNVnator should be able to get the chromosome lengths from your sam header. Try without the -genome option. Also, where is the bam file? From CNVnator: "Chromosome names and lengths are parsed from sam/bam file header. Using -genome option one can overwrite this default behavior." Step 1: Extract ...
written 13 months ago by rbagnall1.2k

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Teacher 5 hours ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
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Scholar 11 months ago, created an answer that has been accepted. For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: How to extract specific chromosome from vcf file
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