The cluster is, I did saw processes to become I/O starved on largeĪlso, consider that most tools that perform association testing can Try PLINK 1.9 orĪs for “The computational facility I'm using should not limit the speed of an operation.”,ĭepending on how disk data moves in/out of slave nodes and how busy If my memory serves me well, qctool manages to strip SNPsįairly quickly, but is super slow to remove samples.
Successful in chopping pieces of bgen files using qctool in a timely Have you tried first stripping the SNPs, then stripping the samples?Įver since working with the imputed data from the UKB I was never I assume you’re working with the latest version? chunk data for re-encoding) - this can be
Qctools alternative software#
Your downstream software supports zstd compression. I typically use the options -bgen-compression zstd -bgen-bits 8 now, If you have to subset and want to use QCTOOL - some things to try are: Inclusion/exclusion list instead, if your analysis software supports ) It is therefore definitely worthĬonsidering not subsetting samples but using a sample (ByĬontrast you can subset SNPs very quickly without recompression usingīgenix. The design of BGEN means that when you subset samples the data has toīe recompressed - this is essentially what makes this slow. I contacted the QCTOOL team directly and received this response: "QCTOOL is a command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data"
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Or any other ideas on why it's running so slowly?Īlternative suggestions on how to process these files would be appreciated for example, although I would prefer to use QCTOOL perhaps I have to use PLINK.Have I made any mistakes in my qctool query?.The computational facility I'm using should not limit the speed of an operation. It is currently processing SNPs at a rate of 1.2/s (e.g. excl-samples /path_to/samples_to_rem.txt My command is pretty basic I’m filtering out a list of SNPs and samples: /path_to/qctool \ bgen files from UK Biobank, however they seem to be processing very slowly.
I’m currently using QCTOOL v2 to process imputed.
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