Strelka
Strelka identifies single nucleotide variants (SNVs) and small indels using the following steps:
| • | Read filtering—Filters out reads that fail quality checks. |
| • | Indel calling—Identifies a set of possible indel candidates and realigns all reads overlapping the candidates using a multiple sequence aligner. |
| • | SNV calling—Computes the probability of each possible genotype given the aligned read data and a prior distribution of variation in the genome. |
| • | Indel genotypes—Calls indel genotypes and assigns probabilities. |
| • | Variant call output—Generates output in a VCF file and a compressed genome variant call (gVCF) file. |
For more information, visit https://github.com/Illumina/strelka.