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• Calculate allele frequency for structural variant breakpoints
  I have a list of high quality structural variant breakpoints that are the product of multiple dif...
• Call variant from RNA-Seq data using Haplotypecaller
  My understanding is that Haplotypecaller is specifically designed to call variant from DNA-Seq da...
• How to filter variant calls based on specific reference and alternate allele frequency ratio during variations calling?
  Hi All, I have been working on targeted amplicon sequencing data (>200 samples). I use GATK f...
• Differences in RNAseq Variant Calling and Allele Specific Expression
  Dear community Using the GATK's tools "haplotypecaller" and "ASEReadCounter" it is possible to p...
• MLE Approach: Calculate LD (r^2) from unphased data
  Hello, I have several population samples, and was able to align my illumina reads to a reference...
• Question about homozygous concept in a paper sentence
  Hello I am reading a paper that is about a software tools VarScan2. In that context, There is a...
• Allele frequency calculation
  I have ~200 exomes which includes related and unrelated individuals. I have done the joint genoty...
• The problem with sensitivity analysis of somatic variant caller
  Hello! I'm working on somatic variant identification from cancer samples. So, I try to simulate...
• Reference Allele Bias
  Dear community members, I do not work with SNVs directly and I can not check this myself. But I ...
• Variant allele frequency
  Can we adjust variant allele frequency in any of the tools like VarScan2, Mutect etc..
• tools to calculate Exac population specific frequency
  HI, I have 500+ MAF files of exome sequencing. I want to get the allele frequency for all popula...
• Why most of alternative alleles are the alleles with major frequency?
  I find set of SNPs that in 4 different population have same minor allele frequency and also same ...
• How To Cluster Data That Contains Minor Allele, Somatic And Germline Frequencies
  Please help. I am new in field and do not know how we can distinguish between somatic and germlin...
• how to use existed database to filter snps in vcf with MAF
  I am reading a research paper that uses GATK to call variants and filtration. > Annotated var...
• VCF validation error:Ref allele mismatch?
  Hello All, I am working on submitting novel SNPs to dbSNP. When I use their online VCF validator...
• Varscan mpileup2snp parameters
  Dear all, I wish to use mpileup2snp to call SNPs. I am confused by two of the parameters --min-...
• Filter a VCF using fields stored in a different VCF
  Question: Is there a way to filter variants in a VCF based on fields stored in a different VCF w...
• IGV not highlighting possible variants
  Surely this is trivial, but I have looked everywhere and I cannot find the answer... IGV sometim...