User: rbagnall

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rbagnall1.1k
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Posts by rbagnall

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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 3 months ago by rbagnall1.1k
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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 3 months ago by rbagnall1.1k
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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 3 months ago by rbagnall1.1k
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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 4 months ago by rbagnall1.1k
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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 5 months ago by rbagnall1.1k
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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 6 months ago by rbagnall1.1k
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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 14 months ago by rbagnall1.1k
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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 15 months ago by rbagnall1.1k
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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 16 months ago by rbagnall1.1k
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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 18 months ago by rbagnall1.1k

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Scholar 3 months ago, created an answer that has been accepted. For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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