Tag: qctool v2

QCTOOL v2

Obtaining QCTOOL QCTOOL is available either as binaries or as source code. The recommended approach is to download and compile the QCTOOL source code on the machine(s) you will be working on. However, for convenience a small number of precompiled binary packages are provided below. These provided as-is and will…

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Using QCTOOL v2 to process UK Biobank .bgen files

Using QCTOOL v2 to process UK Biobank .bgen files – why so slow? 0 I’m currently using QCTOOL v2 to process imputed .bgen files from UK Biobank, however they seem to be processing very slowly. Is this normal? My command is pretty basic; I’m filtering out a list of SNPs…

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vcf to bgen conversion using qctool v2 yields 0 snps

Hi all, I have a vcf file that was extracted from UKB data using qctool (v2.0.6-Ubuntu16.04-x86_64) and contains data in the GP format. This contains a bunch of SNPs from a single chromosome. ❱ wc -l chromosome1.vcf 260 chromosome1.vcf Then I try to convert this file to .bgen again using…

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