User: rbagnall

gravatar for rbagnall
rbagnall1.1k
Reputation:
1,140
Status:
Trusted
Location:
Australia
Last seen:
10 hours ago
Joined:
5 years, 9 months ago
Email:
r*******@hotmail.com

about me

Posts by rbagnall

<prev • 91 results • page 1 of 10 • next >
0
votes
1
answer
469
views
1
answers
Comment: C: snpEff inappropriate interpretation of variants?
... Yeah, possibly. It may be a default annotation of an important amino acid residue. ...
written 5 months ago by rbagnall1.1k
2
votes
1
answer
469
views
1
answers
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 5 months ago by rbagnall1.1k
1
vote
2
answers
380
views
2
answers
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 5 months ago by rbagnall1.1k
0
votes
1
answer
312
views
1
answers
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 6 months ago by rbagnall1.1k
0
votes
1
answer
286
views
1
answers
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 7 months ago by rbagnall1.1k
1
vote
2
answers
401
views
2
answers
Answer: A: Human Mitochondrial Variants Annotation
... Try [Mitomaster][1]. Select the SNV Query tab and enter variants as shown in the examples on the right hand panel. [1]: http://www.mitomap.org/foswiki/bin/view/MITOMASTER/WebHome ...
written 8 months ago by rbagnall1.1k
1
vote
2
answers
563
views
2
answers
Answer: A: Do People Import VCF Files Into Databases? (2016 version)
... [PlinkSeq][1] can read vcf files into a database format, then generate summary stats and extract gene, individual or cohort level data. There is an online tutorial that is helpful. [1]: https://atgu.mgh.harvard.edu/plinkseq/tutorial.shtml ...
written 16 months ago by rbagnall1.1k
0
votes
1
answer
343
views
1
answers
Answer: A: Finding variations in mitochondrial genomes
... A pipeline to sequence mitochondrial genome from off-target exome sequence data: http://www.ncbi.nlm.nih.gov/pubmed/22669646 I found this to work well and the Python scripts are available from the Nature Methods website. There is and another approach, called Mitoseek (not tested by me): http://w ...
written 17 months ago by rbagnall1.1k
4
votes
2
answers
2.7k
views
2
answers
Comment: C: How to extract specific chromosome from vcf file
... grep -w '^#\|^[1-5]' my.vcf > my_new.vcf or if your chromosomes have a chr prefix: grep -w '^#\|^chr[1-5]' my.vcf > my_new.vcf ...
written 18 months ago by rbagnall1.1k
0
votes
1
answer
438
views
1
answers
Comment: C: Number of SNPs captured by targeted sequencing panels
... That would be your best bet, but I don't know if you would reach 10,000 SNPs. Perhaps try intersecting the 4800 TruSight One genes with an exome dataset to see how many SNPs you may expect. ...
written 20 months ago by rbagnall1.1k

Latest awards to rbagnall

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Grep A Pattern From File
Popular Question 7 weeks ago, created a question with more than 1,000 views. For LOD score of a single genotype
Scholar 5 months ago, created an answer that has been accepted. For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: How to extract specific chromosome from vcf file
Guru 21 months ago, received more than 100 upvotes.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Scholar 22 months ago, created an answer that has been accepted. For A: Trouble filtering CDS regions from Nextera Enrichment design
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Appreciated 22 months ago, created a post with more than 5 votes. For A: Grep A Pattern From File
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Free HiSeq X Ten human genome fastq test data
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Scholar 2.6 years ago, created an answer that has been accepted. For A: Trouble filtering CDS regions from Nextera Enrichment design
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Scholar 2.6 years ago, created an answer that has been accepted. For A: Trouble filtering CDS regions from Nextera Enrichment design
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Scholar 3.0 years ago, created an answer that has been accepted. For A: Trouble filtering CDS regions from Nextera Enrichment design
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Scholar 3.2 years ago, created an answer that has been accepted. For A: Trouble filtering CDS regions from Nextera Enrichment design
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Grep A Pattern From File
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
Scholar 3.7 years ago, created an answer that has been accepted. For A: Trouble filtering CDS regions from Nextera Enrichment design
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1749 users visited in the last hour