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• SNPeff method-no reference genome
  Hi there, I would like to know if it is possible to use SNPeff to predict SNPs effect impact on ...
• Advanced use of snpEff
  Hello I have two questions for this wonderful forum: 1- I have results of snpEff (vcf files) b...
• Show warnings and errors in snpeff summary
  Asslamu Alikum I was generated vcf file from bam and fasta file using gatk tool but when it run ...
• several effect for one SNP annotated by SNPeff
  hi i annotated one vcf file using SNPeff and now some SNPs have several effect instead one effec...
• Snpeff for predicting snp effect
  I was using Snpeff for predicting the effect of the snps found in bacterial genomes. there are ac...
• What are SNP effects? in terms of SNPeff output file
  Hi I am calling SNP/Variants from RAN-Seq data. I have followed the GATK pipeline for RNASeq and ...
• Freebayes and snpeff give different number of SNPs
  Hello friends, I called SNPs using Freebayes and also used snpeff to see the effects on the outp...
• Snp-Annotation And Effect Prediction
  I have mapped RNA-seq illumina paired-end reads to reference genome contigs(which is assembled co...
• number of functions is more than namber of variants in snpEff's output
  hi everyone i annotated my vcf file (resulted from samtools) using snpEff and output of snpEff c...
• Predict the effect of SNPs in a VCF file generated using a Trinity assembly
  Is there software or script available to predict the effect of SNPs that have Trinity headers? Re...
• SnpEff question for Variant annotation
  I want to annotate the variant predicted from GRCh38 build. Does SnpEFF use GRCh38?
• Is SNPeff still the standard for variant effect prediction?
  I'm kind of new to this space-- a friend of mine says he uses SNPeff for all his exome annotation...
• How does SnpEff calculate effects?
  In the SnpEff output file you can find possible effects of the variants (frame shift, stop codon ...
• How to seperate vcf annoation info field
  Hello Friends I have created vcf file for my samples using GATK. After variant calling i used snp...
• Annotating the two flanking bases of SNPs in a VCF file (perhaps SnpEff?)
  Hi, I was wondering what tool I could use to annotate a vcf and include the two flanking bases, u...
• SnpEff, Exome Sequencing, Variant Annotation
  I want to annotate my vcf file against COSMIC database using SnpEff. How can we configure SnpEff ...
• snp analysis using a software tool
  i have varient data obtained from a tool that give varients in with refernce to a genome. i had t...