This repositorty contains all the scripts that I used for benchmakring Vaquita. The result was presented in WABI 2017 in Boston.

Prerequeistics

• Variant callers

Name	Reference	Version
Vaquita	source repository	WABI2017
LumpyExpress	Layer et al., 2014	0.2.13
Delly2	Rausch et al., 2012	0.7.3
CREST	Wang et al., 2011	1.0
Pindel	Ye et al., 2009	0.2.5b8
GASVPro	Sindi et al., 2012	Oct1_2013

You can use wrapper scripts for several programs for your conveniecne.

• Simulators

Name	Reference	Version
Mason	Holtgrewe, 2010	2.0.5
ART	Huang et al., 2012	MountRainer-2016.06.05

You can refer my commands for generating simulation datasets in simulations.txt.

• Real datasets

Name	Link or Accession #
Genome in a bottle	ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/technical/svclassify_Manuscript/Supplementary_Information/Personalis_1000_Genomes_deduplicated_deletions.bed
Illumina Platinum Genomes	ERR194147, ERR194160, and ERR194161

Configuration

Please open config.py, and change settings accordingly. For example, you may have to change binary files for variant callers in here.

Run & Reporting

You can refer my command in commands.txt.

Contact

Jongkyu Kim (vaquita_WABI@jongkyu.kim)