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• Using Varscan without a matched normal
  Hi there, I got an extremely incredible use of varscan. You see, typically, we need a matched-n...
• how to interprete the somatic mutations with low frequency in tumor sample compared with the normal one
  I have matched pair samples: tumor and normal sample. I used varscan and mutect to call the somat...
• Variant Filtration And Surprising Results
  Greetings, I have been working on a comparison of a human endocrine cancer, matched with normal ...
• the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?
  Hi, I am new to tumor phylogenetics. I want to call snvs from the tumor cells and using the snv...
• Can we do unsupervised clustering of Varscan output based on variant frequencies?
  Dear All,   I have some queries regarding the Varscan output. I have some varscan output files ...
• Multi-Sample Somatic Mutation Calling
  Hi all! I have 4 pairs of matched tumor/normal exome sequencing experiments. These are from 4 p...
• Music Analysis Workflow
  Hello there, I am pretty new to the cancer field and now try to run MuSiC for WashU to detect si...
• How to get somatic variant from TCGA vcf files
  I want to extract all somatic mutations from TCGA vcf files, I have three sources for each file:...
• Can a normal tissue sequence be used for various tumor samples in Varscan Somatic or GATK MuTect2?
  I have exome sequencing data from tumor samples from mice with only one of them has tumor/normal ...
• Why do people not call normal and tumor variant separately for somatic mutation identification?
  Hello, I have been using VarScan and MuTect to call somatic variants. Lately, of curiosity, I al...
• Calling germline variants from Tumor/Clone pairs to find the somatic mutations of only tumor and only clone from the normal pair
  Dear All,   I have some query regarding mutation call with VarScan2. I have whole exome data fo...
• Why different somatic mutation callers agree so poorly on tumor sample pairs?
  I used Mutect Strelka and Varscan 2 on  multiple nomal-tumor pairs of sequencing data. Default pa...
• how to extract all reads covered at the somatic SNP site that from a BAM file in VCF file with using python?
  HI , I am doing some tumor research. I used GATK to call somatic SNV . now I have the tumor ...
• VarDictJava BED file input Problem
   Hi, I have WGS dataset which are based on TGCA tumor normal samples. I have to call somatic mut...
• Software To Call Somatic Indels?
  I'm looking for a tool to call somatic indels (10-1000bp range, not point mutations) in tumor/nor...
• Extract somatic mutations and germline mutations from variant calling files?
  Hi all, I'm wondering how one can extract germline and somatic mutations from the variants calli...