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• How to consider/get the g. positions for variants in introns?
  Hello All, My query is regarding the genomic positions to be considered for a variant which are ...
• How to convert intronic variants with IVS nomenclatures to their respective nucleotide positions?
  I have few intronic novel variants for which I want to extract the genomic positions using Mutaly...
• Annotation using annovar
  Dear All, I would like to address certain queries of mine. I have been using Annovar for a while...
• How to interprete PlasmidSeeker results when you have some plasmid clusters?
  I've been interested in plasmid detection in bacterial genomes. I tried plasmidfinder and this so...
• determination of alternate splicing events from assembled transcripts
  hi all, I want to determine alternative splicing events for my assembled transcripts (i used st...
• Somatic variant call
  I have matched samples from three tissues of an individual and I am trying to prioritize the path...
• Tools for predicting the protein altering effects of the variants from EXON-seq data
  Hi Say I have a lot of variants including INDELS, SNVs, SNPs, etc from the exon-seq dataset. Now...
• Variants in Exon or Intron
  After getting the variants using gatk pipeline, how can I know if the variant is in an exon or in...
• Variant Annotation - Which Transcript(S) Are The Best Representatives Of The Variant?
  I would like to learn what are the rules one should use while annotating variants, specifically t...
• Skipping The Local Realignment Around The Indels And Rather Aligning The Mapped Reads On The Exonic Region.
  I have a query that we do the local realignment around the indels with the known sites because it...
• GSEA with variant proportions as input
  Hello All, I am interested in using using variant proportions as input to perform Gene Set Enric...
• Quantification of interested genes using bowtie and eXpress
  Currently, I am interested in several (around 100) genes in fish and would like to investigate th...
• variant calling using reference transcriptome
  Hi, Is there any tool which uses a reference transcriptome to call variants instead of a referen...
• Mimic WES on WGS data + A comprehensive list of coding regions in the most biologically relevant transcripts
  Dear peers, I have the results of WGS in the FASTQ, BAM and VCF formats to be interpreted using ...
• Calculating Ds/Dn Ratio Through Contig Snp Annotation
  I am newbie to NGS I have mapped my illumina reads to non-model assembled reference contigs. By ...
• Finding exons and introns sequences
  Hello everybody!! I have to analyze exons' and intron's sequences of many organisms. ...
• How to filter and annotate variants for influenza virus?
  Hi All, I have a vcf file from GATK tool. I would like to filter and annotate the variants. Can ...
• any tools for annotating "canonical splice site variants"
  Similar posts have been put up in the past by other users but I haven't yet found any helpful ans...
• How can i increase variants accuracy?
  I want to increase accuracy in the variants using multiple variants calling tools such as Varscan...
• Transcript Specif qPCR primer
  I have a gene which is having 10 transcript variants. However, only 4 transcripts are protein cod...
• variant calls which are important
  I used a VCF file to filter somatic mutations based on various various filters as suggested by ve...
• snpEff inappropriate interpretation of variants?
  I have RNA-seq datasets, and I applied GATK variant calling procedure for RNA-seq (https://softwa...
• calling the variants in a sample with respect to other sample
  I have two different samples, say **WT (wildtype)** and **A6 (Crispr mutated)**. (samples are il...