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/CRAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF.

• Version: 0.4.5
• Added: February, 2023
• Link: https://github.com/pjedge/longshot

See which versions are available:

$ module avail longshot

Load one version into your environment and run it:

$ module load longshot/0.4.5
$ longshot

Notes from the sysadmin during installation.

$ cd /tmp
$ wget https://github.com/pjedge/longshot/archive/refs/tags/v0.4.5.tar.gz
$ tar xf v0.4.5.tar.gz
$ cd longshot-0.4.5
$ sudo dnf install rust cargo
$ cargo install --path .
$ sudo mkdir -p /export/apps/longshot/0.4.5/bin
$ sudo cp ~/.cargo/bin/longshot /export/apps/longshot/0.4.5/bin