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Germlin_+_Somatic_Callers.md

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Variant Identification

Germline + Somatic Callers

  1. [VarScan 2] (http://massgenomics.org/varscan)
  • Description: identify germline variants, private and shared variants, somatic mutations, and somatic CNVs; detects indels
  • Input: SAMtools pileup
  • Output: VCF
1. **[BAYSIC] (http://genformatic.com/baysic/)** * Description: Bayesian method; combines variant calls from different methods (GATK, FreeBayes, Atlas, Samtools, etc) * Input: VCF format from one or more variant calling programs * Output: VCF file containing integrated set of variant calls 1. **[MSIsensor] (https://github.com/ding-lab/msisensor)** * Description: Microsatellite instability detection; C++ program, detects somatic and germline variants in tumor-normal paired data * Input: BAM index files (normal and tumor) * Output: 1. **[Beagle version 4] (http://faculty.washington.edu/browning/beagle/beagle.html)** * Description: software package: genotype calling, phasing, imputation of ungenotyped markers, and identity-by-descent segment detection:unsure if this one is in the right category; genotype calling, phasing, imputation of ungenotyped markers, and identity-by-descent segment detection; * Input: VCF * Output: VCF 1. **[QuadGT] (http://www.iro.umontreal.ca/~csuros/quadgt/)** * Description: software package, SNV calling from normal-tumor pair and two parent genomes; quantifies descent-by-modification relationships; Written in Java * Input: BAM files (parsed by Picard/Samtools API) * Reference Genome; FASTA * Output: VCF 1. **[RAREVATOR] (http://sourceforge.net/projects/rarevator/)** * Description: RAre REference VAriant annotaTOR; command line; “identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data”; Bayesian genotype likelihood model * Input: BED or VCF files from GATK * Output: two VCF files (one for SNVs, one for Indels) 1. **[Scalpel] (http://scalpel.sourceforge.net/)** * Description: Used for detecting indels in a reference genome; performs localized micro-assembly of specific regions of interest; can do single, de novo, somatic reads; requires that raw reads are aligned with BWA * Input: BAM * Output: either VCF or ANNOVAR 1. **[SOAPsnp] (http://soap.genomics.org.cn/soapsnp.html)** * Description: based on Baye’s theorem; calls consensus genotype * Input:SOAP short read alignment results * Output: GLF, option of flat tabular format 1. **[VariantMaster] (http://sourceforge.net/projects/variantmaster/)** * Description: “extract causative variants for monogenic and sporadic genetic diseases”; uses ANNOVAR; * Input: BAM or VCF files (from SAMtools, GATK) * Output: