Tag: .bim

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 •…