Tag: .fam

Changes in ped and map files in PLINK

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…

Continue Reading Changes in ped and map files in PLINK

Updating hg 18 .bim file with lifted .map and .bed file

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….

Continue Reading Updating hg 18 .bim file with lifted .map and .bed file

Bcftools equivalent of vcftools conversion to ped & map

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…

Continue Reading Bcftools equivalent of vcftools conversion to ped & map

Merge only bim files with plink

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…

Continue Reading Merge only bim files with plink

Plink Alternative Phenotype File Columns not being Read

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…

Continue Reading Plink Alternative Phenotype File Columns not being Read

SNP extraction

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…

Continue Reading SNP extraction

Question about ROH analysis by Plink 1.9

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…

Continue Reading Question about ROH analysis by Plink 1.9

Phenotype file for eQTL analysis using GEMMA

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…

Continue Reading Phenotype file for eQTL analysis using GEMMA

What does .bim .bed .fam stands for?

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 •…

Continue Reading What does .bim .bed .fam stands for?