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• Extracting specific SNPs from VCF
  Hi, **How should I extract specific SNPs from VCF file (30x). What is the standard way of doing ...
• Snpeff for predicting snp effect
  I was using Snpeff for predicting the effect of the snps found in bacterial genomes. there are ac...
• Automatic Detection And Annotation Of Bacterial Snps
  Hi all, I am working on 10 bacterial genomes (1 reference and 9 mutant) sequenced by Illumina te...
• Functional Score Annotation Bacteria (VCF)
  Hi .. I am searching for alternatives to variant annotation in bacteria. Specifically, add functi...
• Need suggestions in subsetting the Annovar annotated VCF file
  Hello Everyone, I am fairly novice Bioinformatician. I need some help and suggestions on tools t...
• Best way to create a multi-sample VCF
  Hello, I have about 150 bacterial whole genome sequences that I would like to use to create a ...
• Comparison and Visualization of VCF derived from Two Genomes (tolerant and susceptible) #DNA-Seq
  Hi Friends, I already have two VCF files generated using SAMtools (susceptible and tolerant) of ...
• ABH to VCF for annotation
  I am having a set of GBS (SNPs) in ABH format which i corrected by ABH genotypeR and used for QT...
• snps causing protein change
  I have one VCF file which contain SNPs calls with annotation. Currently, I am trying to figure ou...
• Convert association data from gwas catalog to vcf format
  Hi there, I have a tsv file from GWAS-Catalog like this one in tsv format: ftp://ftp.ebi.ac.uk/pu...
• Input file for MDR(Multifactoral dimension reduction) for exome data
  I am new to human whole exome sequencing data analysis. After I am done with whole exome analysis...
• output feature/gene name from a known base position
  Just a little background so that I can put my question into context. I have a list of SNPs and I ...
• Fourfold degenerate codons in VCF File
  Hi, I want to extract the SNPs that have fourfold degenerate codons in a VCF file annotated by S...
• calculate the number of Non-Synomous and Synonymous SNP sites
  Hi, I have a VCF containing the SNP information between the two genotypes of interest and using t...
• retain UMIs when converting bam to vcf file
  I have 10X data that I would to extract all of the SNPs for a very specific site on one gene to a...
• RNA-seq SNP analysis
  Hello, I generated VCF and .bam files from transcriptomes files of C.remanei. Now, I want to do ...
• How To Perform A Fst (Fixation Index) Calculation Over A Vcf File Using A Sliding Window?
  Hello Everyone, I have 2 vcf files, each one contains snps from samples from a single different ...
• How can you update position field in a VCF?
  I am attempting to LiftOver a set of vcf files from hg19 to hg38. I attempted to use the `picard ...
• how to find out protein changes from SNPs
  I already got VCF files with annotated SNPs, but I also need to know whether protein structure ch...
• Using SnpEff on Galaxy
  I have been trying to use SNPeff on Galaxy to annotate a vcf file. I am working with the genome o...
• Filter SNPs in multiple-sample vcf based on the snps of two samples
  Hello all, I have a `.vcf` file with ~96 samples which were called using `freebayes`. This `.vc...
• pulling snps from vcf file using ids
  Is there a command line in vcf tools to pull a subset of snps out of a vcf file based on their rs...