User: omid.alavijeh

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Posts by omid.alavijeh

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Comment: A: Extract several columns from a VCF file
... I've edited my answer above ...
written 4 months ago by omid.alavijeh40
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Comment: C: Faster filtering of vcfs using split-vep over filter_vep
... Hi @finswimmer, I work in an airlock environment so can't bring data out but it looks like this (taken from another site but basically the same). head my.vcf ##fileformat=VCFv4.0 ##VEP="v91" time="2018-01-04 23:07:28" cache="/home/davetang/.vep/homo_sapiens/91_GRCh37" ensembl-varia ...
written 4 months ago by omid.alavijeh40 • updated 4 months ago by finswimmer13k
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Answer: A: Extract several columns from a VCF file
... Do you mean you have the SNP IDs? bcftools view -i ID==@text file_of_SNP_IDs yourvcf > output.vcf Further to your question I think you want: bcftools view -s sample1,sample2 file.vcf > filtered.vcf bcftools view -S sample_file.txt file.vcf > filtered.vcf ...
written 4 months ago by omid.alavijeh40 • updated 4 months ago by RamRS27k
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Faster filtering of vcfs using split-vep over filter_vep
... Dear Biostars, I am trying to filter a multi-sample vcf which has been annotated with VEP in order to get a set of rare likely deleterious calls. However, the file is very large and using "filter_vep" is taking a very long time per file (>5 days per chromosome on a HPC environment). I have been ...
split-vep vcf vep bcftools written 4 months ago by omid.alavijeh40
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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 months 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 months 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 months 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 months 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 months 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 5 months ago by omid.alavijeh40

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