User: omid.alavijeh

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Posts by omid.alavijeh

<prev • 19 results • page 1 of 2 • next >
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Comment: C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
... Correct! Apologies if that was too vague. I have amended by question accordingly. ...
written 4 days ago by omid.alavijeh40
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Comment: C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
... Dear RamRS, It is a multi-sample vcf. Whilst it may contain mutations I can assure you it has not been mutated. ...
written 4 days ago by omid.alavijeh40
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Comment: C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
... That's quite the one liner! Thanks I'll give it a go. All the best. ...
written 4 days ago by omid.alavijeh40
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Comment: C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
... Yup - its a multi sample vcf chunked by region of the genome. ...
written 4 days ago by omid.alavijeh40
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BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a region
... Hello! I have a regular multi-sample VCF from which I am looking to find individuals that have >1 HET call in the same gene. The vcf is chunked so relatively small in size (with the gene of interest in the chunk)/ Does anyone have a one liner for such a task with bcftools or even R? Many tha ...
bcftools written 4 days ago by omid.alavijeh40
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Comment: C: Creating a genotype matrix for BeviMed
... Thanks German, would there be an easy way of making such a file from a VCF? ...
written 14 days ago by omid.alavijeh40
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(Closed) Creating a genotype matrix
... Dear Biostars community, I am trying to run "Bevimed" - https://cran.r-project.org/web/packages/BeviMed/vignettes/Intro.html. A Bayesian approach to rare variant analysis on a case control cohort. I have the cases and controls in a merged per chromosome format as well as in plink binary files. As ...
bcftools genotype written 26 days ago by omid.alavijeh40
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Creating a genotype matrix for BeviMed
... Dear Biostars community, I am trying to run "Bevimed" - https://cran.r-project.org/web/packages/BeviMed/vignettes/Intro.html. A Bayesian approach to rare variant analysis on a case control cohort. I have the cases and controls in a merged per chromosome format as well as in plink binary files. ...
genome bioinformatics bayesian snp written 28 days ago by omid.alavijeh40
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Filtering large VCFs by allele freqency using bcftools split-vep function
... Dear Biostars community, I have a large VCF file that has been annotated using VEP. The intrinsic filtering function built into VEP whilst effective is very slow across large VCFs from my experience. I have been playing around with the spli-vep plug-in on bcftools and found it to be much faster, ...
split-vep bcftools vep written 3 months ago by omid.alavijeh40
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Comment: C: Filtering multiple single person structural variant VCF files by type of SV
... Thanks again Reza for taking the time to reply. I actually have a multi-callVCF file already but was more interested in looking at SV variation between my cohort so thought generating individual patient VCF files by type of SV would be informative. Many thanks Omid ...
written 3 months ago by omid.alavijeh40

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