User: anamaria

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anamaria100
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Posts by anamaria

<prev • 92 results • page 1 of 10 • next >
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Why ukb_gen_samples_to_remove function takes forever to execute?
... Hello, I was running: >library(ukbtools) > dim(main_data) [1] 403974 1095 > dim(data) [1] 107124 5 > remove_fin=ukb_gen_samples_to_remove(data, main_data$eid, cutoff = 0.0884) But ukb_gen_samples_to_remove() takes hours to execute. I am running this wit ...
ukbtools written 6 days ago by anamaria100
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I/O error when converting Plink files to Merlin format for imputation using MACH?
... Hello, as I understand in order to do imputation on MACH I have to convert my plink files to Merlin format. I was using mega2 but I am getting this I/O error. I do have space on my disk and I do have write permissions so that should not be the problem. Errors I am seeing are these: DB sqlite ...
mega2 imputation mach written 11 days ago by anamaria100
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Comment: C: [SOLVED] Get LD data for any two SNPs
... Hi Mike, I have exactly the same issue like you and I would like to use your code to compare LD between two lists of SNPs. Can you please tell me where I can find that code? ...
written 16 days ago by anamaria100
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extracting SNPs from .vcf file along with CHR and POS
... Hello, I download file 00-All.vcf.gz from https://ftp.ncbi.nih.gov/snp/pre_build152/organisms/human_9606_b150_GRCh37p13/VCF/ I need to extract a list of SNPs (which I put in META_rs) from there long with their CHR# and position I am doing this: vcftools --gzvcf 00-All.vcf.gz --snps META_rs ...
vcftools written 19 days ago by anamaria100
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How to resolve "Error: All remaining samples for --glm phenotype 'pheno' are cases" in Plink?
... Hello, I was running GWAS via: plink2 --threads 24 --pfile temporary17 --recover-var-ids NVCFchr17.vcf.gz 'force' --pheno pheno_hes_nephropathy_hba1c.txt --pheno-name pheno --covar pheno_hes_nephropathy_hba1c.txt --covar-name sex,age,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,TD,array,HBA1C --g ...
plink written 4 weeks ago by anamaria100
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Comment: C: relationship between PI_HAT and --king-cutoff coefficient?
... Thanks for sharing that. One thing is unclear to me is it necessary to run: plink --bfile output8 --genome --grm-cutoff 0.1 --make-bed --out output9 after I did run this bellow? plink2 --bfile output7 --king-cutoff 0.0884 plink2 --bfile output7 --remove plink2.king.cutoff.out.id --make-bed --out ou ...
written 9 weeks ago by anamaria100
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relationship between PI_HAT and --king-cutoff coefficient?
... Hello, as I see from plink documentation to keep only distantly related samples PI_HAT=P(IBD=2)+0.5*P(IBD=1)=0.125 according to this table 1 https://www.sciencedirect.com/science/article/pii/S0002929714004273 but I am unable to find a table which would compare plink --king-cutoff coefficients with ...
pihat plink ibd written 9 weeks ago by anamaria100 • updated 9 weeks ago by Sam2.9k
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Comment: C: Ibd (Identity By Descent) And The Chosen Value Of Pi_Hat
... Hi Matt, Can you please let me know if I want my Pihat < 0.1 Can I set in plink --rel-cutoff 0.1, or in plink2 --king-cutoff 0.1 ? If not what would be the way to do this? Thanks ...
written 10 weeks ago by anamaria100
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Comment: C: Extract a list of SNPs from a BCF file
... I am doing this on some cluster so ...but anyway thank you so much for debugging tips! ...
written 11 weeks ago by anamaria100
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Comment: C: Extract a list of SNPs from a BCF file
... it's this one: bcftools --version bcftools 1.10.2-32-ge677391 Using htslib 1.10.2-46-g9a10355 Copyright (C) 2019 Genome Research Ltd. ...
written 11 weeks ago by anamaria100

Latest awards to anamaria

Popular Question 19 days ago, created a question with more than 1,000 views. For Manhattan plots and linkage disequilibrium heatmap
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Manhattan plots and linkage disequilibrium heatmap
Popular Question 5 months ago, created a question with more than 1,000 views. For Manhattan plots and linkage disequilibrium heatmap
Popular Question 7 months ago, created a question with more than 1,000 views. For How to replace rownames in one data frame with column in another data frame
Popular Question 7 months ago, created a question with more than 1,000 views. For How to order bars in barplot in ggplot?
Student 11 months ago, asked a question with at least 3 up-votes. For Manhattan plots and linkage disequilibrium heatmap
Scholar 12 months ago, created an answer that has been accepted. For A: Issues with col2rgb

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