User: rbagnall
rbagnall • 1.2k
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Posts by rbagnall
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3
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1
answer
104
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... 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
rbagnall • 1.2k
1
vote
1
answer
159
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1
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... 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
rbagnall • 1.2k
2
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1
answer
159
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1
answer
... 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 ...
written 6 weeks ago by
rbagnall • 1.2k
• updated
6 weeks ago by
Emily_Ensembl ♦ 15k
0
votes
1
answer
242
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1
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... 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
rbagnall • 1.2k
1
vote
2
answers
187
views
2
answers
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
rbagnall • 1.2k
0
votes
1
answer
774
views
1
answers
... Yeah, possibly. It may be a default annotation of an important amino acid residue. ...
written 11 months ago by
rbagnall • 1.2k
2
votes
1
answer
774
views
1
answers
... 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
rbagnall • 1.2k
1
vote
2
answers
586
views
2
answers
... 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
rbagnall • 1.2k
0
votes
1
answer
527
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1
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... 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
rbagnall • 1.2k
0
votes
1
answer
429
views
1
answers
... 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
rbagnall • 1.2k
Latest awards to rbagnall
Good Answer
10 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Grep A Pattern From File
Popular Question
7 months ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
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
Guru
2.2 years ago,
received more than 100 upvotes.
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For Free HiSeq X Ten human genome fastq test data
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
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created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
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3.7 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
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