User: Casbon

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Casbon3.2k
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Posts by Casbon

<prev • 116 results • page 1 of 12 • next >
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Comment: C: Splitting A Vcf File
... No need to if the header doesn't include tabs, which it normally doesn't ...
written 7.2 years ago by Casbon3.2k
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Answer: A: Validation Of Sequence Clustering
... I used SCOP superfamilies. As Larry says, you can't go wrong with a manually curated structural database when testing a sequence-based clustering. ...
written 7.2 years ago by Casbon3.2k
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Why Are The Samtools/Bcftools Pv4 T-Tests One Sided?
... From the mpileup page, we have the definition: PV4: P-values for 1) strand bias (exact test); 2) baseQ bias (t-test); 3) mapQ bias (t); 4) tail distance bias (t) Looking at the source for this t-test (I couldn't find any further documentation), we can can see on line 61: if ( ...
vcf bcftools mpileup statistics written 7.2 years ago by Casbon3.2k • updated 7.2 years ago by lh331k
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Answer: A: Splitting A Vcf File
... cut -f1-9,n file.vcf Where n is the column of the sample you want. ...
written 7.2 years ago by Casbon3.2k
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Comment: C: Why Does Samtools/Bcftools Give Incorrect Genotypes And Innacurate Quality Score
... Well, as I understood it, the point is to avoid genotype calling in low coverage data. Since this it high coverage, this makes bcftools inappropriate? ...
written 7.2 years ago by Casbon3.2k
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Answer: A: Genome Browser Figure
... It's not a browser, but genometools produces really nice output: http://genometools.org/images/cnn_large.png ...
written 7.2 years ago by Casbon3.2k
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Why Does Samtools/Bcftools Give Incorrect Genotypes And Innacurate Quality Scores?
... I have resequenced a target region in depth and called with samtools with default parameters (except depth). I find the calls to be pretty inaccurate. For example, two of these samples are from the 1000 genomes pilot 2 YRI family. I have used the 1000 genomes calls to check the genotypes at rs734 ...
vcf samtools bcftools genotyping written 7.2 years ago by Casbon3.2k • updated 7.2 years ago by lh331k
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Comment: C: Can A Biomarker Be Exclusively Licensed?
... Casey, I think you're wrong. The legal protection of SNPs is clearly hugely important for for bioinformatics, which four upvotes clearly agree. I think I'm leaving and not coming back after this and your RTFM nonsense as well. Goodbye, Biostar! ...
written 7.4 years ago by Casbon3.2k
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Comment: C: Can A Biomarker Be Exclusively Licensed?
... Thanks Pierre, I suppose it is August in France ;) ...
written 7.4 years ago by Casbon3.2k
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Comment: C: Can A Biomarker Be Exclusively Licensed?
... Thanks, Pierre! ...
written 7.4 years ago by Casbon3.2k

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