Tag: .bim

I’m new to PLINK and I would like to obtain a file with SNPs in approximate linkage equilibrium. Here is my script and the outputs of each step. If someone could tell me if there is an error in the script because at…

Alternatives to snpflip to find ambigious and flipped snps 0 Hello everyone, I having an issue with strand flips when trying to perform imputation. In the past on an old HPC I used it supported snpflip, a tool which would recognize ambigious snps as well as snps that have been…

Hi Chris,         This problem seems so silly but I just got stuck here for a long time.         I tried to extract a set of SNPs (I’m pretty sure they all appear in the .bim file) and rename their IDs with –set-all-var-ids, and…

PLINK Error: No valid entries in –score file 0 Hi, I ran this command on plink1.9 to calculate the poligenic score. plink –vcf sample –score output.txt 1 2 3 –out poligenic_results – output.txt: ID ALT UKB-b-15541 rs10399793 C 0.000345793 rs2462492 T -0.00027716 – sample.vcf: #CHROM POS ID REF ALT QUAL…

Association Analysis with Plink error 3 1. this is my phenotype file (called outputfile.txt in command line use): FID IID Cadmium_Chloride Caffeine Calcium_Chloride Cisplatin Cobalt_Chloride Congo_red Copper Cycloheximide Diamide E6_Berbamine Ethanol Formamide Galactose Hydrogen_Peroxide Hydroquinone Hydroxyurea Indoleacetic_Acid Lactate Lactose Lithium_Chloride Magnesium_Chloride Magnesium_Sulfate Maltose Mannose Menadione Neomycin Paraquat Raffinose SDS Sorbitol…

I want to compare/validate variants called from sequencing data with array (plink format) variant data. I converted the plink files (.bim, .bed, and .fam files) with plink1 to vcf files. plink –bfile prefix_plink –recode vcf-iid –out prefix_out However, the plink vcf files have “I” and “D” values for INDEL variants…

plink –bfile {chr1_exomes} –update-ids {new_IIDs_A} –make-bed –out {updated_chr1_exomes_A} plink –bfile {chr1_exomes} –update-ids {new_IIDs_B} –make-bed –out {updated_chr1_exomes_B} plink –bfile {updated_chr1_exomes_A} –bmerge {updated_chr1_exomes_B}.bed {updated_chr1_exomes_B}.bim {updated_chr1_exomes_B}.fam –make-bed –out {merged_chr1_exomes_A_B} Original data: ID1, ID2, … New data: ID1_A, ID1_B, ID2_A, ID2_B, … Would updating the IDs of the .fam file be enough in this…

Beagle log not matching SNP data 0 Hello, I am trying to impute the genotypes of 32 individuals to WGS with Beagle 5.4 and I found inconsistences between beagle logs and my SNP data. I run Beagle with this: java -Xss51m -Xmx64g -jar beagle.22Jul22.46e.jar gt=genotype_Chr1.vcf ref=training_ref_Chr1.vcf.gz out=genotypeChr1_imputed These are the…

How to salvage incomplete PLINK .bed files? 1 I converted a number of large SeqArray (.gds) files into PLINK binary format, but when the .bed files were written to storage, it appears that many of them became truncated. I would like to salvage as much data as possible from these…

Using -r2 in plink1.9 with .bim file that has CHR:POS entries 0 Hello, I have the following line of code: /Plink1.9/plink –bfile “${PLINK_REF_PANEL}/${chrom}”.final \ –r2 \ –ld-window 10000 \ –ld-window-r2 ${PLINK_MIN_R2} \ –keep “${PLINK_REF_PANEL_KEEP}” \ –out “${out_prefix}” \ –ld-snp-list “${SNAPTMP}/SNAP.input.proxy” \ > plink.${chrom}.r2.out #/dev/null And I have a .bim file…

Hi everyone, I have a binary PLINK fileset in which alleles are coded 1/2 and failed calls are denoted by 0. The 1/2 format is based off the A/B format, where 1 = A and 2 = B. I want to recode the alleles as ACGT. I would like to…

PLINK1.9 check sex problem 0 Hello! I use plink1.9 with –check-sex option to check sex in data with only one sample. I use –read-freq with a file contained frequencies of variants from chrX of 1000G (obtained by –freq). My problem is that for all samples I have F=-1 and SNPSEX=2….

Dear community I’m currently trying to try a GWAS for case control study using PLINK using whole exome VCF files. I understand that I need to convert these VCF files into PLINK’s binary format (bed/bim/fam) before I can proceed with the GWAS. From my literature I have to manually create…

1. Introduction 2. Basic information 3. Downloads and general notes 4. Command reference table 5. Basic usage/data formats 6. Data management 7. Summary stats 8. Inclusion trim 9. Population stratification 10. IBS/IBD estimation 11. Bond 12. Family-based community 13. Permutation process 14. LD calculations 15. Multimarker tests 16. Conditional haplotype…

(PLINK): Can’t convert .ped .map into .bim .fam .bed. Why? 0 Hi. I have a .ped and .map that I have previously created from a .vcf. Note that this VCF was NOT created by aligning reads to a reference genome, but rather by de novo (using the “STACKS” pipeline). I…

Hi, I’m running a big SNP database (160GB vcf file) I pruned with plink; plink –vcf SNPs_clean1.vcf –allow-extra-chr –indep-pairwise 50 10 0.1 –out SNP_50_10_01 It starts running producing the temporary files and the output files prune.in and prune.out). In the log file it shows having filtered the variants, 49595998 of…

Error opening .bim file while running Admixture 2 Hi All! While running the following command: for K in 1 2 3 4 5; do admixture –cv hapmap3.bed $K | tee log${K}.out; done Such error came up: Estimation of standard errors disabled; will compute point estimates only. Error opening .bim file!…

How to generate a .raw file from vcf in plink 1 Hi all. I am trying to convert my vcf file to a readable format in R using plink. Specifically, I want a .raw file to follow up the workflow of a recent paper. I have tried: plink –vcf myfile.vcf.gz…

I am getting the following output after running Plink. Why am I getting the following warning for some SNP markers? I have checked those markers, they are not triallelic. Then where is the error? How can I fix it? Scanning .ped file… Possibly irregular .ped line.  Restarting scan, assuming multichar…

Hi everyone, I was trying to run ADMIXTURE using a merged vcf file with 82 samples. I pruned the data using a set of plink command: plink –vcf 82_samples.vcf.gz –make-bed –double-id plink –bfile 82_samples –indep-pairwise 50 5 0.5 –out 82_samples_pruned plink –bfile plink –extract 82_samples_pruned.prune.in –make-bed –out 82_samples_pruned Then I…

Using LiftOver to change genomic build 0 Hi, all – Two questions about using LiftOver: The .bed file changes after using LiftOver. Correct me if I’m wrong, but I can just use the .bim and .fam file from before LiftOver as those do not change? I have used LiftOver to…

make BED file from existing BIM and FAM files 2 Hello everyone, I have a set on .bim and .fam files by chr and I would like to create the corresponding .bed files. I tried using plink but they require .map or .pgen files as input and I don’t have…

Hello, I am hoping somebody with experience with plink could help. I am trying to generate plink .bim, .fam and .bed files from a .vcf (one with variants filtered out and one that keeps the variants) and have toyed around with a couple of different commands that I found on…

Changes in ped and map files in PLINK 1 Hello all, I want to do QC with Plink but I want to have the changes of QC in my ped and map files after QC. I used the items below but received .bim, .fam, and .bed files. My ped and…

Updating hg 18 .bim file with lifted .map and .bed file 0 Hello, I am trying to update rsids in an hg18 .bim file with an hg38.bed and hg38.map file. I’ve tried the following: system(“./plink –file plink_hg38 –make-just-bim –out newBim –allow-extra-chr”) but got the error: Error: Failed to open plink_hg38.ped….

Bcftools equivalent of vcftools conversion to ped & map 1 I am converting a VCF to ped & map thus in vcftools vcftools –gzvcf ZZZZZTYT.vcf.gz –plink –out ZZZZZTYT which works fine. However, I have been searching and searching, can bcftools do the same with a bcf? bcftools • 103 views…

Merge only bim files with plink 0 Hello For the same dataset they provide a single BED and FAM files for all the chromosomes. However, the BIM files are split in chromosomes. I would like to generate the VCF file with the genotyping calls of all chromosomes but I need…

I am a new user of PLINK and am analysing some SNP data for the first time. After creating a .bim file with $ plink –file my_data –make-bed I notice that for several SNPs my data is different from dbSNP e.g. rs145496306: BIM file: A G dbSNP: G>A,T rs3813199: BIM…

SNP extraction 0 I want to extract specific SNPs of interest i have in a text file into an additive genetics model so that each SNP can be in a 0/1/2 format for each subject using genetics info in from PLINK (.bed, .bim, and .fam files). How can i do…

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

Note1 – Previous version: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old) Note2 – this data is for hg19 / GRCh37 Note3 – GRCh38 data is available HERE The tutorial has been updated based on the 1000 Genomes Phase III imputed genotypes. The original tutorial was…

What does .bim .bed .fam stands for? 1 I have a hard time differentiating these files, maybe understanding the acronyms could help. If I’m right .ped is from pedigree and .bed is a strange way to say ‘binary-pedigree’. The others are obscure. plink fam bim bed • 21 views •…