![]() ![]() g * additive_beta (g=1) * heterozygote_beta. > The risk score for each individual is the sum over SNPs of the genotype times the effects, i.e. > The -risk-score feature is 'beta' status so please do apply a liberal dose of sanity checking, > The 'risk_score_identifier' column is used to give the risk score a name multiple risk score definitions can be provided in the same file (with different names) and they will get output in seperate output columns. > SNPID rsid chromosome position alleleA alleleB risk_score_identifier additive_beta heterozygote_beta. > Sorry, this is wrong: the file should have 9 named columns: > The file must have 8 named columns, SNPID rsid chromosome position alleleA alleleB additive_beta heterozygote_beta. > sample index GRS_risk_score GRS_risk_score_count > # -snp-match-fields position (user-supplied) chr22impv1_all_snps.bgen (user-supplied) > Number of samples in input file(s): 152249. > - computing these risk scores: GRS(1 SNPs) > SampleSummar圜omponent: the following components are in place: > # of samples after filtering: 152249 (0 filtered out). > ( 738 snps) "./chr22impv1_all_snps.bgen (bgen v1.1 152249 unnamed samples compressed)" > Input SAMPLE file(s): "BiobankCADdef_AGE.sample" > SNPID rsid chromosome position alleleA alleleB risk_score_identifier additive_beta heterozygote_beta The positions and alleles match the data. > I’m trying out a toy example using a score made of one SNP in chr22 on UK Biobank data, but I’m getting zeros in the final score (see below). > On May 25, 2017, at 4:43 AM, Gad Abraham wrote: I have a naive question, does qctool’s -risk-score do the same thing as plink’s -score (main difference is that they are compatible with different file formats)? In the end I did not pre-filter SNPs or samples - I set samples to NA within the phenotype file, and used a SNP inclusion list in the second stage of SAIGE with the flag idstoIncludeFile.Email discussion lists for the UK Education and Research communities 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 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" 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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