Tag: .fam

Processing WES VCF for case control GWAS analysis

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…

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KING kinship inference error

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…

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Can’t convert .ped .map into .bim .fam .bed. Why?

(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…

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plink produces does pruning according to log file but prune.in is full of dots

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…

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LD pruning for SNP markers

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…

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Using LiftOver to change genomic build

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…

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make BED file from existing BIM and FAM files

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…

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VCF to Plink files

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…

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Plink duplicate ID

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…

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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…

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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….

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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…

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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…

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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…

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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…

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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…

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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…

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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 •…

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