Tag: .fam

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…

KING kinship inference error 2 Hello, I’m trying to use KING for estimating kinship between individuals. I have a vcf file that resulted from a de novo assembly of ddrad seq data. First, I tried to convert my vcf file to .bed file using Plink2.0, but it failed saying that…

(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…

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…

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…

Plink duplicate ID 1 Hi, I’ve converted the reich dataset to plunk format along with my vcf file provided from my full genome, I merged the both together which led to getting an error and output two files. The two files it output was .fam and .missnp, now it tried…

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…

Plink Alternative Phenotype File Columns not being Read 0 Hi, I have a plink alternative phenotype file with the following format: FID IID Phenotype 1 2 1 1 3 0 etc. As outlined in the plink documentation. zzz.bwh.harvard.edu/plink/data.shtml#pheno However, when I run the following command : plink –bfile ../Plink_Files/plink –logistic…

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…

Phenotype file for eQTL analysis using GEMMA 0 Hello All, I appreciate it if someone could direct me in this regard. I am running eQTL analysis using GEMMA software. I have corrected the expression file with all samples (280 samples) and the genotype file is (170). I have a couple…

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 •…