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• Merge Samtools and Freebayes vcf files
  Hi, I am analyzing presence of variants in exonic regions of 10 genes. I have sequencing data fo...
• merging two different datasets of different samples and variants
  Hello All, I am vinay kumar reddy nannuru, i have a vcf file of 92 samples with 14000 variants i...
• Indel concordance from different VCF files
  Hello, I am trying to compare SNP's and INDELS from two VCF files that belong to the same sample...
• Best tool to merge .vcf files from different variant callers?
  I have vcfs from the same samples that have variants called from one of three callers. I want to ...
• Filter a VCF using fields stored in a different VCF
  Question: Is there a way to filter variants in a VCF based on fields stored in a different VCF w...
• Merge vcf files of structural variants
  Hi, I have many single sample vcf files containing structural variants. I'm trying to merge all ...
• Tools for just generating a file including all shared variants in all VCF files
  Hello, I have 4 VCF files which represent variants files from 4 different samples. 1) I do not wa...
• Genotype is changing after merging multiple vcf files using bcftools merge command
  I have 3 vcf files containing 10, 15 and 20 different individuals in each file. The merging comma...
• Bcftools equivalent of vcf-merge R?
  Hi everyone, I need to merge two VCF files which contain different variants, something I can do ...
• Merging BAM or VCF files, whats the difference?
  Hello everybody. I have two main set of file to analyze, the end goal is SNP discovery and haplo...
• VCF merge and VCF intersect
  I want to use vcf-merge or vcf-intersect on multiple vcf files and then filter the variants based...
• Comparing VCFs constructed from mapping to different reference genomes
  Hi, I am comparing variant calling pipelines from two authors who have used different versions of...
• VCFTools vcf-merge not merging all files
  Hi All, I am trying to use vcf-merge. However on my test batch of 6 files, only the first two me...
• Consensus VCF file from several variant callers
  Hi all, I want to do a consensus VCF file with only the variants that have been called by two var...
• Merging VCFs: Illumina/GATK and LoFreq
  I have VCFs from a number of different tumor samples sourced mostly from two different variant ca...
• Change ALT field in VCF
  Hi all, I have 2 vcf files for the same positions but with different individuals which I would l...
• Merge VCF files with diploid reference calls in different order for same positions (e.g. TC vs CT)
  I'm trying to use VCF tools to merge two large VCF files for the same species. The problem I'm ha...
• VCF comparison: shared variants
  Hi! Is there a way to compare two vcf not only by position, but also for the genotypes? I want t...
• How to merge VCF files, and consider variants within a set distance as one
  I'm trying to merge several VCF files, each with inserts from a different individual. There are i...
• Combining two VCFs each with own set of mutations
  I have two VCF files, each containing somatic mutation calls on each chromosome (ie. the VCFs are...
• Combine several VCF files
  I've performed variant calling with two callers. One calls haplotypes and other calls mutations a...
• merging vcf by vcftools
  Dear All I have tried to merge two vcf files by using vcf-sort, gzip, tablix followed by vcf-merg...