Toolkit Comparison

	A	B	C	D	E	F	G	H	I	J	L
1	Category	Feature	PLINK (2.0)	Hail	Glow	Scikit-allele	SNPRelate	GENESIS	GWASTools	bigsnpr
2	Data Representation	Polyploidy	O	X	X	X	O	O	O	O	X = First-class support
3		Multi-allelic variants	X*	X	X	X	O	O	O	O	X* = Not available in last major release (1.9 for PLINK)
4		Phased Calls	X*	X	X	X	O	O	O	O	x = Less than first-class support
5		Allosomes	X*	X	O	O	O	O	X	O
6		Genotype Probabilities	X*	X	x	O	x	O	O	x	O = No support
7		WGS/WES Stats	O	X	X	O	x	O	O	O	<blank> = Haven't looked yet
8	Linkage Disequilibrium	LD Matrix	X	X	O	X	X	O	O	X
9	Linkage Disequilibrium	LD Pruning	X	X	O	X	X	O	O	X	Highlighted boxes = Core groups of functionality without which even basic GWAS QC and analysis becomes difficult
10	Relatedness	IBS	X	X	O	O	X	O	O	O
11		GRM	X	X	O	X	X	O	O	X	Red = Notable deficiencies within a toolkit relative to others
12		Relatedness Pruning	X	O	O	O	O	O	O	O	Green = Notable features that differentiate a tookit from others and potentially enable new capabilities or more effective/efficient workflows
13	Kinship Estimation	IBD	X	X	O	O	X	O	O	x
14		PC-Relate	O	X	O	O	O	X	O	O
15		KING (homo/robust)	X*	O	O	O	X	O	O	x
16	Population Decomposition	PCA	X	X	O	X	X	X	O	X
17		PCA projection	X	x	O	X	X	O	O	X
18		Approximate PCA	X*	O	O	X	O	O	O	X
19		PC-AiR	O	O	O	O	O	X	O	O
20		F-statistics	X	O	O	X	X	O	O	O
21	Association	RVAS	O	X	O	O	O	X	O	O
22		Univariate Linear/Logistic Regression	X	X	X	O	O	X	X	X
23		Univariate Penalized Regression	X*	X	O	O	O	X	X	O
24		Linear Mixed Models	O	X	O	O	O	X	O	O
25		Chi-Square	X	O	O	O	O	O	O	O
26		Multivariate Regression (PRS)	O	O	O	O	O	O	O	X
27	Liftover	Coordinate Liftover	O	X	X	O	O	O	O	O
28	Liftover	Variant Liftover	O	O	X	O	O	O	O	O
29	Statistics	HWE	X	X	X	X	O	O	X	O
30		Inbreeding Coefficients	X	X	O	X	X	O	X	O
31		Allele Frequencies	X	X	X	X	X	O	X	X
32		Call Rate	X	X	X	X	X	O	X	O
33		ROH (LOH)	X	O	O	X	O	O	X	O
34		Selection	O	O	O	X	O	O	O	O
35		Mendel Errors	X	X	O	X	O	O	X	O
36		Genomic Control (lambda gc)	X	X	O	O	O	O	O	x
37	Inference	Haplotype Phasing	O	O	O	x	O	O	O	O
38		Genotype Imputation	O	O	O	O	O	O	O	x
39		Missingness Imputation	X	X	O	O	X	X	X	X
40		Sex	X	X	O	O	O	O	O	O
41	Import	PLINK	X	X	X	O	X	O	O	X
42		vcf	X	X	X	X	X	O	O	x
43		bgen	X	X	X	O	O	O	O	X
44		bcf	X	O	O	O	O	O	O	O
45		gen	X	X	O	O	X	O	O	O
46		gds	O	O	O	O	X	X	X	O
47	Export	PLINK	X	X	O	O	O	O	X	X
48		vcf	X	X	X	X	O	O	X	O
49		bcf	X	O	O	O	O	O	O	O
50		gen	X	X	O	O	O	O	O	O
51		bgen	X	O	X	O	O	O	O	O
52		gds	O	O	O	O	X	O	X	O
53	Scalability	Multi-core	O	X	X	X	X	x	O	X
54	Scalability	Distributed	O	X	X	x	O	O	O	O
55	Misc	Sample Clustering	X	O	O	O	X	O	O	O
56		Multi-allelic variant splits	O	X	X	O	O	O	O	O
57		Genome Annotation	O	X	O	O	O	O	O	O
58		Call Concordance	O	X	O	O	O	O	O	O
59		De novo variant calling	O	X	O	O	O	O	O	O
60	Meta	Links	SS				SS		SS	SS
61		Published	2007				2012		2012	2018
62		Semantic Scholar citations	12,940				454		64	11
63		Semantic Scholar citations/yr	995				57		8	6
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