Error No File Plink.fam Exists
Contents |
Formats | Data management | Summary stats | Filters | Stratification | IBS/IBD | Association | Family-based | Permutation | LD calcualtions | Haplotypes | Conditional tests | Proxy association |
Plink Recode
Imputation | Dosage data | Meta-analysis | Result annotation | Clumping | Gene plink missing genotype Report | Epistasis | Rare CNVs | Common CNPs | R-plugins | SNP annotation | Simulation | Profiles | plink 2 ID helper | Resources | Flow chart | Misc. | FAQ | gPLINK
1. Introduction 2. Basic information Citing PLINK Reporting problems What's new? PDF documentation 3. Download andPlink Download
general notes
Stable download Development code General notes MS-DOS notes Unix/Linux notes Compilation Using the command line Viewing output files Version history 4. Command reference table List of options List of output files Under development 5. Basic usage/data formats Running PLINK PED files MAP files Transposed filesets Long-format filesets Binary PED files Alternate phenotypes Covariate files Cluster files Set files 6. DataDbsnp
management
Recode Reorder Write SNP list Update SNP map Update allele information Force reference allele Update individuals Write covariate files Write cluster files Flip strand Scan for strand problem Merge two files Merge multiple files Extract SNPs Remove SNPs Zero out sets of genotypes Extract Individuals Remove Individuals Filter Individuals Attribute filters Create a set file Tabulate SNPs by sets SNP quality scores Genotypic quality scores 7. Summary stats Missingness Obligatory missingness IBM clustering Missingness by phenotype Missingness by genotype Hardy-Weinberg Allele frequencies LD-based SNP pruning Mendel errors Sex check Pedigree errors 8. Inclusion thresholds Missing/person Allele frequency Missing/SNP Hardy-Weinberg Mendel errors 9. Population stratification IBS clustering Permutation test Clustering options IBS matrix Multidimensional scaling Outlier detection 10. IBS/IBD estimation Pairwise IBD Inbreeding Runs of homozygosity Shared segments 11. Association Case/control Fisher's exact Full model Stratified analysis Tests of heterogeneity Hotelling's T(2) test Quantitative trait Quantitative trait means Quantitative trait GxE Linear and logistic models Set-based tests Multiple-test correction 12. Family-based association TDT ParenTDT Parent-of-origin DFAM test QFAM test 13. Permutation procedures Basic permutation Adaptive permutation max(T) permutation Ranked permutation Gene-dropping Within-cluster Permuted phenotypes files 14. LD calculations 2 SNScripting Unix shell scripting - KSH, CSH, SH, BASH, PERL, PHP, SED, AWK and shell scripts and shell scripting languages here. Search Forums Show Threads Show Posts Tag Search Advanced Search Unanswered Threads Find All Thanked Posts Go to Page... learn linux and unix commands - unix shell scripting PLINK help Shell Programming and Scripting Thread Tools Search this Thread Display Modes #1 08-31-2012 smitra Registered User Join Date: Aug 2012 Last Activity: 30 June 2013, 6:51 AM EDT Posts: 28 http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Thanks: 15 Thanked 0 Times in 0 Posts PLINK help Hi Plink users, I am very new in GWAS and decided to use PLINK for this. But I am struggling with file formats. I have one exome data with 200000 SNPs in it. But it is in .txt format. But all the necessary fields are there in different columns. Can you please suggest me how http://www.unix.com/shell-programming-and-scripting/198895-plink-help.html I can create the plink .bed file? Is there any direct way to create .bed file from .txt? I tried to create a .bim and a .fam file following the instruction in PLINK website Binary files (BED/BIM/FAM) Is there any way to create .bed file from these two (.bim & .fam) files? Please let em know. Thanks a lot, Suparna. Remove advertisements Sponsored Links smitra View Public Profile Find all posts by smitra #2 08-31-2012 Corona688 Mead Rotor Join Date: Aug 2005 Last Activity: 13 October 2016, 7:04 PM EDT Location: Saskatchewan Posts: 21,548 Thanks: 997 Thanked 3,955 Times in 3,676 Posts I was really confused until I figured out there's two applications named plink, and you weren't talking about an ssh client What, exactly, did you try? What, exactly did it do? Did you or did you not succeed in making the bim and fam files? What syntax is your input file? "text" doesn't mean much, since lots of them appear to be text of different arrangement. The Following User Says Thank You to Corona688 For This Useful Post: smitra(08-31-2012) Remove advertisements Sponsored Links Corona688 View Public Profile
testers [Jump to search box] General usage Citation instructions Standard data input PLINK 1 binary (.bed) Autoconversion https://www.cog-genomics.org/plink2/input behavior PLINK text (.ped, .tped...) VCF (.vcf{.gz}, .bcf) Oxford (.gen{.gz}, .bgen) 23andMe text Generate random Unusual chromosome IDs Recombination map Phenotypes Covariates Clusters of samples Variant sets Binary distance matrix IBD report (.genome) Input filtering Sample ID file Variant ID file Cluster membership Set membership Attribute-based Chromosomes SNPs only error no Simple variant window Multiple variant ranges Sample/variant thinning Covariates (--filter) Missing genotypes Missing phenotypes Minor allele frequencies Hardy-Weinberg Mendel errors Quality scores Relationships Main functions Data management --make-bed --recode --output-chr --zero-cluster --split-x/--merge-x --set-me-missing --fill-missing-a2 --set-missing-var-ids --update-map... --update-ids... --flip --flip-scan --keep-allele-order... --indiv-sort --write-covar... --{b}merge... Merge failures VCF reference merge --merge-list --write-snplist error no file --list-duplicate-vars Basic statistics --freq{x} --missing --test-mishap --hardy --mendel --het/--ibc --check-sex/--impute-sex --fst Linkage disequilibrium --indep... --r/--r2 --show-tags --blocks Distance matrices Identity-by-state/Hamming (--distance...) Relationship/covariance (--make-grm-bin...) --rel-cutoff Distance-pheno. analysis (--ibs-test...) Identity-by-descent --genome --homozyg... Population stratification --cluster --pca --mds-plot --neighbour Association analysis Basic case/control (--assoc, --model) Stratified case/control (--mh, --mh2, --homog) Quantitative trait (--assoc, --gxe) Regression w/ covariates (--linear, --logistic) --dosage --lasso --test-missing Monte Carlo permutation Set-based tests REML additive heritability Family-based association --tdt --dfam --qfam... Report postprocessing --annotate --clump --gene-report --meta-analysis Epistasis --fast-epistasis --epistasis --twolocus Allelic scoring (--score) R plugins (--R) Secondary input GCTA matrix (.grm.bin...) Distributed computation Command-line help Miscellaneous Tabs vs. spaces Flag/parameter reuse System resource usage Pseudorandom numbers Resources 1000 Genomes phase 1 Teaching materials Gene range lists Functional SNP attributes Errors and warnings Output file list Order of operations For developers GitHub repository Compilation Core algorithms Partial sum loo