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• Intronic Variant Filtering
  Hello all, I want to filter variants based on their genomic location. For example RSID rs1086380...
• Too many intronic variants in RNASeq, is this ok?
  Hi every one I did GATK somatic mutation pipeline, then I annotated the resulted mutect2 vcf wi...
• How to retrieve SNP numbers from the VCF then find information about them whether they are intron on exon variant ?
  I have a VCF file for SCN9A gene which has multiple SNP's in it. I want to retrieve those SNP num...
• Transcription of ncRNA
  Is ncRNA transcripted only from introns? If not, is ncRNA transcripted also from exons or a comb...
• Non-Overlapping, de-deduplicated BED file download with exons as separate records
  I would like to have a table of all genes (hg19 assembly, RefSeq) with their respective exons as ...
• How To Understand Some Annotated Terms Made By Annovar
  Hi, I have question about annotation by Annovar. It is a little bit confusing for me now when I n...
• Query regarding reporting of RNA seq variants
  1)For data derived from RNA sequencing and aligned to the genomic reference sequence, applicatio...
• Exome variants limited only to the first half of a gene? Technical error?
  Hi, We have performed an exome for a genetically heterogeneous disorder. There is a certain ge...
• SPANR result interpretation
  Hi, I have an intronic variant which lies ~70bp upstream of an exon and I have used splicing-bas...
• Analysis of introns and exons
  I picked Calpastatin sequences. How do I determine which areas exons and introns Which is? Is the...
• the location of TFBS in genome / binding affinities caused by SNP
  I have an annotated set of SNPs and I would like to explore the difference in the binding affinit...
• Any Tool Which Remark The Boundries Like Regulatory, Intron And Exon In Gene Sequence
  I have some gene sequences, retrieved from GWAS study and want to know the SNP variant is present...
• How to write HGVS nomination for noncoding intergenic variants
  I want to generate HGVS nomination for each variant I have on a file. For the coding ones it is e...
• Determine Variant Location From Vcf
  hi all, i have a rather large VCF files with about 2.8 million variations. i want to know if each...
• gene based annotation : Database or live computation ?
  There are several annotation database for annotation variants. Like dbNSFP, dbSNP, cosmic.... I ...