User: rbagnall

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rbagnall1.3k
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Posts by rbagnall

<prev • 101 results • page 1 of 11 • next >
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Answer: A: Looking for walkthrough guide on Rare Variant Association Analysis
... Have a look at [PLINK/SEQ][1] tutorials. They give a walk through of the steps involved in exploring variation in vcf files, including different types of association tests. You should probably start at the PLINK/SEQ_101 and the extended tutorial, which have lots of informative steps on setting up t ...
written 3 months ago by rbagnall1.3k
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Answer: A: Detecting Homozygous Insertion from Sanger Seq
... Yes. 1. The Sanger sequencing trace will look very 'clean', with only single allele peaks on the chromatogram at each nucleotide (see the first 8 nucleotides of ATpoint's figure above), but there will be some additional bases compared to the reference at the site of the insertion. Some other point ...
written 3 months ago by rbagnall1.3k
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Comment: C: no successful variants lifted over from hs37d5_plusRibo_plusOncoViruses_plusERCC
... Do the chromosome names in hs37d5 look like 1, 2, 3 etc, and in GRCh38 look like chr1, chr2, chr3? ...
written 4 months ago by rbagnall1.3k
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... hmm, try = "Pathogenic" rather than ~ "Pathogenic" ...
written 4 months ago by rbagnall1.3k
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Comment: C: Find Intersections Between ClinVar Track and VCF In IGV
... The clinvar.vcf needs to be bgzip compressed and tabix indexed first. uncompress then bgzip gunzip grch37_clinvar.vcf.gz | bgzip > grch37_clinvar.bgzip.vcf.gz tabix index tabix -p vcf grch37_clinvar.bgzip.vcf.gz view alleles in grch37_clinvar.bgzip.vcf.gz that have pathogenic in the CLNSI ...
written 4 months ago by rbagnall1.3k
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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 4 months ago by rbagnall1.3k
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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 5 months ago by rbagnall1.3k
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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 5 months ago by rbagnall1.3k • updated 5 months ago by Emily_Ensembl16k
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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 6 months ago by rbagnall1.3k
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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 7 months ago by rbagnall1.3k

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Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
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Popular Question 11 months ago, created a question with more than 1,000 views. For LOD score of a single genotype
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Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Scholar 3.4 years ago, created an answer that has been accepted. For A: Trouble filtering CDS regions from Nextera Enrichment design
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