A list of awesome tools and pipelines that calls variants from NGS data. I listed them into categories based on their original design or implementation (in published papers) to analyze specific data type.
- freebayes: Bayesian haplotype-based polymorphism discovery and genotyping.
- LoFreq: LoFreq models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population.
- VarScan 2: Detects somatic mutations and copy number alterations (CNAs) from exome data.
- GATK
- DISCOVAR: A new variant caller capable of assembling small genomes.
- Platypus: Platypus is designed for efficient and accurate variant-detection.
- SGA
- samtools
- DISCOSNP:DISCOSNP detects isolated SNPs from any number of read datasets, without a reference genome.
- VarCap: a workflow for the reliable prediction of different types of variants even at low frequencies
- freebayes: Bayesian haplotype-based polymorphism discovery and genotyping.
- LoFreq: LoFreq models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population. VarScan 2: Detects somatic mutations and copy number alterations (CNAs) from exome data.
- breseq: breseq finds mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.
- GATK: use
HaplotypeCaller, calls germline SNPs and indel. - samtools
- pilon: Find variation among bacterial strains, including large event detection
- KvarQ: Targeted and Mapping-Free Variant Calling in FastQ Reads of Bacterial Genomes.
- Snippy: Rapid bacterial SNP calling and core genome alignments.
- parsnp: Core genome alignment, SNP detection, and phylogeny.
- DISCOSNP:DISCOSNP detects isolated SNPs from any number of read datasets, without a reference genome.
- NASP: NASP is flexible in terms of data input types, job management systems, diversity of supported tools and output format.
- ISGPipeline: creates a matrix of SNPs across multiple taxa.
- REALPHY: uses multiple references. Can take raw fastq files. Produces a tree.
- SPANDx: for haploid whole genome re-sequencing datasets. Can take raw sequences.
- LoFreq: LoFreq models sequencing run-specific error rates to accurately call variants occurring in <0.05% of a population.
- ViVaMBC: estimates viral sequence variation in complex populations. Optimized to call variants at the codon level.
- VirVarSeq: a low frequency virus variant detection pipeline.
- QQ-SNV: Single Nucleotide variant detection at low frequency.
- Platypus: Platypus is designed for efficient and accurate variant-detection.
Disclaimer: Some of these tools might have already been used in categories where its not listed. It is likely not listed due to lack of updating this list or it did not show up in the first page of google result or was not exclusively mentioned in the abstract or readme files.