User: PhiPhi

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PhiPhi0
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Posts by PhiPhi

<prev • 5 results • page 1 of 1 • next >
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Comment: C: How to read variants into R from large dataset using VariantAnnotation
... Version 1.28.11 works much better! Thanks a lot!! ...
written 5 months ago by PhiPhi0
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Comment: C: How to read variants into R from large dataset using VariantAnnotation
... Thank you for your timely reply! No, it won't work if I specify all samples. This file is from UK-Biobank. ...
written 5 months ago by PhiPhi0
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Comment: C: How to read variants into R from large dataset using VariantAnnotation
... Thank you for your suggestions! I try `VariantAnnotation::readGT()` function which works if I do not specify the variant range and can read in all half million population correctly: vcf.ref.file <- "chr22.vcf.50.header.gz" vcf_rng<-readGT(vcf.ref.file, nucleotides=TRUE, row.names=TRUE ...
written 5 months ago by PhiPhi0
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Comment: C: How to read variants into R from large dataset using VariantAnnotation
... Thank you for the response! I am afraid memory is not a problem. We ran the package in a server with 256GB RAM. We only tried to read 100 markers from 100,000 individuals. Do you have other suggestions? sessionInfo(package="VariantAnnotation") R version 3.5.1 (2018-07-02) Platform: x86 ...
written 5 months ago by PhiPhi0 • updated 5 months ago by Martin Morgan ♦♦ 23k
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How to read variants into R from large dataset using VariantAnnotation
... I am trying to use the Bioconductor library "VariantAnnotation" to read in data from UK BioBank which has around half a million samples. It gives me error message even when I want to read only 50 variants: "Error: scanVcf: scanVcf: scanTabix: (internal) _vcftype_grow 'sz' < 0; cannot alloca ...
software error written 5 months ago by PhiPhi0 • updated 5 months ago by Martin Morgan ♦♦ 23k

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