User: rbagnall
rbagnall • 1.1k
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Posts by rbagnall
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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 12 days ago by
rbagnall • 1.1k
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636
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... Yeah, possibly. It may be a default annotation of an important amino acid residue. ...
written 8 months ago by
rbagnall • 1.1k
2
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1
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636
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1
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... 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 8 months ago by
rbagnall • 1.1k
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... 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 8 months ago by
rbagnall • 1.1k
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429
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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 9 months ago by
rbagnall • 1.1k
0
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1
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365
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1
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... 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 10 months ago by
rbagnall • 1.1k
1
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526
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...
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 11 months ago by
rbagnall • 1.1k
1
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650
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... [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 19 months ago by
rbagnall • 1.1k
0
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1
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380
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... 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 20 months ago by
rbagnall • 1.1k
4
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3.5k
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... 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 21 months ago by
rbagnall • 1.1k
Latest awards to rbagnall
Popular Question
4 months ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
Scholar
8 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Commentator
21 months ago,
created a comment with at least 3 up-votes.
For C: How to extract specific chromosome from vcf file
Guru
24 months ago,
received more than 100 upvotes.
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Free HiSeq X Ten human genome fastq test data
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
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3.2 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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3.9 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
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