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• How to add trio information to VCF or PED format (to compute Mendel error in Plink)
  I have some VCF files, and a spreadsheet with trio information (child, father and mother IDs). I ...
• SNP IDs changed when making .ped files using PLINK
  I have data on genetic variants for multiple individuals for a family in the form of a .vcf file....
• Combining Data Of Multiple Vcfs Into One.
  I have a number of VCF files, where each VCF file possesses variant data for a single patient (th...
• Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking for family relationships a priori?
  I'm trying to convert a VCF of ~15K samples (~4K families) into PLINK binary format to check for ...
• Individual IDs in .vcf format are not the same as in the original plink format that I converted to .vcf using plink/seq
  I converted from plink file format to vcf file format using plinkseq by following instructions of...
• Best way to convert VCF to PLINK file format and merge chromosomes?
  I am trying to convert the 1000G genotypes into plink format so I can try to run a PCA.  I used ...
• How To Convert Vcf File To Plink Ped Format?
  Hi! Biostar readers This is my first post to Biostar, I have a VCF file containing variants, i ...
• How To Split Multiple Samples In Vcf File Generated By Gatk?
  I did variant calling using BWA + PiCard + GATK and have just got the filtered VCF files from GAT...
• Hard filtering results of vcf file for multiple samps
  Hi all, Assuming, there are multiple samples, say 500 samples, which used for variant calling by...
• Questions on tagging low qual variants and DP filtering on a joint VCF (generated by GATK GenotypeGVCFs)
  Hi Folks, I got two questions according to joint VCF (multiple samples) need your help. I ne...
• How to handle missing values when combining multiple VCF files?
  I have ~200 VCF files. Each of them contains Whole Exome Sequencing information for one sample. I...
• PLINK assoc input: can it be two vcf files case/control?
  Hello, I want to do an association test with plink. I have two vcf files: one has all common var...
• How to combine a multi sample VCF from multiple sample VCF and interpret a multi sample vcf of bacterial genome?
  I used GATK HaplotypeCaller for Variant calling of 2300 MTB strains. Now i want to make it a mult...
• Comparing VCF files between two groups (15 vcf files against 15 vcf files)
  Hello, I have 15 vcf files for one type of population and 15 vcf files for another type. I want ...
• vcf to venn diagram
  Hi, I tried to reproduce this [article](https://justinbagley.rbind.io/2018/07/25/how-to-find-comm...
• Is there a way to force a specific order for variants in a PLINK file that have the same chromosome and bp position?
  I have a VCF that I am reading into PLINK. This VCF has many variants that are redundant in posi...
• Plink formatting issues map file has zeros for chromosome and physical position
  Hi, I have a vcf file that I am converted into ped and map files for plink. When I look at the m...
• Validate the VCF file by freebayes
  Hello, I had run two types of variant calling using Freebayes and Mpileup with several individual...