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• ACMG 59 genes
  Hi, I am new to this bioinformatics and i have one doubt. Why we are only focusing 59 genes ment...
• How to find nu. of variants present in a gene for my Exome seq. sample
  Dear All, I'm new to NGS and learning bioinformatics analysis in NGS. I have generate vcf file u...
• Will it be right to select a random threshold in GWAS to declare significant peaks?
  I run gwas for 7 traits of plant leaves, with 886930 snps, after that I got result, in which p-va...
• How does OMIM select the clinically associated variants (SNPs)?
  Hi all, I know that OMIM shows some, and not all, of the clinical variants of an SNP for a gene....
• Filter variants based on multiple condition
  I have four vcf files (two patient and two control samples). I want to select variants present in...
• Selection of variants based on candidates
  HI all, We have performed several RNAseq experiments with multiple replicates and different cond...
• Same DNA sequence code change in different genes
  If the same DNA sequence code change is present in different genes, does that mean they represent...
• Variation and Exon number
  Hi, I have different stop gain and stop loss variants. I want to check in which exon these varia...
• Usefulness of clustering experimental groups to visualize outliers and heterogeneity
  Hello, Pardon the newbie question. I have a set of DEGs from two experimental groups in comparis...
• Filtering somatic variants (annotated VCF files)
  Hello! I am currently in the process of filtering gene variants in an annotated VCF file. The var...
• How should I calculate the variant density, per kb for a gene, for two different groups in a case/control study?
  I have variant data for a group of people. Some of those people have a disease. I'm trying to cre...
• Intersect multiple VCF files
  Hey guys, Is there any way to use `bedtools intersect` on multiple VCF files to get only variant...
• How to split Double or Multiple Nucleotide Polymorphisms (DNP) into Single Nucleotide Polymorphisms (SNP)?
  Greetings, I have a vcf file with some variants as the following: NC_002516.2 6892 . ...
• Re-Annotating An Existing Gff File?
  Among my data I have a GFF file that was generated by an external service I have no control on. T...
• IGV and Variant Call
  Hello guys, I have two bam files that I load in IGV. Each of those bams I did Variant Calls on t...
• Variants selection with Gene Ontology
  Hi I have SNP data from a DNA array , with GeneOontology tool on R , I selected SNP on DNA repai...
• How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median
  I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then...
• GATK variant calling
  Hi there, I am working with GATK best practices pipeline and am at a point of making a joint cal...
• Non-coding variants in TCGA data
  Hi Everyone, I have been analysing a few cancer samples. I have found some interesting non-coding...