Test output format

The output of stoat test is written to a file stoat.assoc.pvalues.tsv.gz. The output varies slightly depending on which test is being run.

Column	Present for which test?	Content
CHR	all	Chromosome name
START_OFFSET/END_OFFSET	all	Start/end position of the snarl. If it's a nested snarl not on the reference, this will be the coordinates of the lowest ancestor snarl on the reference.
START_NODE/END_NODE	all	Identifier for the snarl, as the start and end nodes with orientations pointing into the snarl
ALLELE_LENGTHS	all	Comma-separated list of the lengths of each allele. For complex variants (which contain nested variants), there could be multiple possible lengths so they are represented as a range (min/max). A SNP will appear as 1,1[,1...]. A simple INDEL will have one zero-length allele and the other non-zero.
DEPTH	all	How deeply nested is the variant? 1 for top-level variant, 2 for nested within a top-level variant, etc.
P	not chi2	P-values calculated using the regression model.
P_FISHER/P_CHI2	chi2	P-values calculated using Fisher's exact test (if two alleles) or the Chi-squared test.
ALLELE_COUNT	not chi2	For each allele, how many haplotypes take this allele. Comma separated list.
ALLELE_COUNT_PER_PHENO	chi2	For each allele (comma-separated), how many haplotypes in each phenotype group take this allele (colon-separated). Each entry is formatted as X:Y,X':Y',... where X:Y represents the counts for one path (allele), with X being the count of samples in group 0 and Y in group 1.
GENE	eqtl	Gene name

Example of an output file

Example of the output for a binary phenotype (provided with -b):

#CHR	START_POS	END_POS	START_NODE	END_NODE	PATH_LENGTHS	P_FISHER	P_CHI2	ALLELE_COUNT_PER_PHENO	DEPTH
ref	247411	247411	>4271	<4260	0,616	0.368	0.3172	107:97,93:103	1
ref	247411	247411	>4270	<4267	1,1	0.1532	0.1447	14:24,79:79	2

Example of the output for a quantitative phenotype (-q option):

#CHR	START_POS	END_POS	START_NODE	END_NODE	PATH_LENGTHS	P	ALLELE_COUNT	DEPTH
ref	244656	244796	>4238	>4236	0,140	0.5142	22,378	1
ref	244553	244553	>4236	>4234	0,182	0.7975	348,52	1

Example of the output for an eQTL analysis (-e option):

#CHR	START_POS	END_POS	START_NODE	END_NODE	PATH_LENGTHS	GENE	P	ALLELE_COUNT	DEPTH
1	100000	100001	>2	>5	1,1	gene_80	0.2039	201,199	1