start:software:topical:lifesciences:ngs:varian_calling_tools

# Variant Calling Tools

The Broad Institute's Genome Analysis Toolkit (GATK) offers a broad variety of tools, particularly variant discovery and genotyping. Modules on MOGON can be found as1):

bio/GATK

Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs). Modules on MOGON can be found as2):

bio/Longshot

Varlociraptor is a program designed for variant calling using unified statistical models.

Modules on MOGON can be found as3):

bio/Varlociraptor

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