Finemapping results format

The finemapping results come from two different finemapping methods: FINEMAP and SuSiE.

The purpose of finemapping is to find the set of 1 or more variants most likely to be responsible for the association at that locus. This set of likely variants is referred to as a "credible set". You can read more about the motivations for finemapping in the main concepts: Finemapping.

Most severe transcript is chosen by first taking the most severe among canonical protein coding transcripts, if no canonical transcript exists, then first (random) other protein coding transcript is chosen corresponding to the most severe annotation. Precedence of severity is chosen according to Ensembl Variant Effect Predictor (VEP) default.

SuSiE outputs

Both 95% credible set and 99% credible sets are provided. The file with _99 contains 99% credsets as below.

PHENONAME.SUSIE.cred.bgz and PHENONAME.SUSIE_99.cred.bgz

Contains credible set summaries from SuSiE fine-mapping for all genome-wide significant regions.

Column	Description
region	Region for which the fine-mapping was run
cs	Running number for independent credible sets in a region
cs_log10bf	Log10 Bayes factor comparing the solution of this model (cs independent credible sets) to cs -1 credible sets.
cs_avg_r2	Average correlation R2 between variants in the credible set
cs_min_r2	Minimum R2 between variants in the credible set
cs_size	How many SNPs the credible set contains

PHENONAME.SUSIE.cred.summary.tsv and PHHENONAME.SUSIE_99.cred.summary.tsv

Summary of credible sets where the top variant for each CS is included.

Column	Description
trait	Phenotype
region	Region for which the fine-mapping was run
cs	Running number for independent credible sets in a region
cs_log10bf	Log10 Bayes factor comparing the solution of this model (cs independent credible sets) to cs -1 credible sets.
cs_avg_r2	Average correlation R2 between variants in the credible set
cs_min_r2	Minimum R2 between variants in the credible set
low_purity	boolean (TRUE, FALSE) indicator if the CS is low purity (low min R2)
cs_size	How many SNPs the credible set contains
good_cs	boolean (TRUE, FALSE) indicator if this CS is considered reliable. IF this is FALSE then top variant reported for the CS will be chosen based on minimum p-value in the credible set, otherwise the top variant is chosen by maximum PIP
cs_id	Credible set ID
v	Top variant (chr:pos:ref:alt)
p	Top variant p-value
beta	Top variant beta
sd	Top variant standard deviation
prob	overall PIP of the variant in the region
cs_specific_prob	PIP of the variant in the current credible set (this and previous are typically almost identical)
0..n	Configured annotation columns. Typical default most_severe, gene_most_severe giving consequence and gene of top variant

PHENONAME.SUSIE.snp.bgz and PHENONAME.SUSIE_99.snp.bgz

Contains variant summaries with credible set information.

Column	Description
trait	Phenotype
region	Region for which the fine-mapping was run
v, rsid	Variant IDs
chromosome	Chromosome no.
position	Position on the chromosome
allele1	Major allele
allele2	Minor allele
maf	Minor allele frequency
beta	Original marginal beta
se	Original standard error
p	Original p-value
mean	Posterior mean beta after fine-mapping
sd	Posterior standard deviation after fine-mapping
prob	Posterior inclusion probability
cs	Credible set index within region
lead_r2	R2 value for a lead variant (the one with maximum PIP) in a credible set
alphax	Posterior inclusion probability for the xth single effect (x := 1..L where L is the number of single effects/causal variants specified; default: L = 10).

PHENONAME.SUSIE.snp.filter.tsv and PHENONAME.SUSIE_99.snp.filter.tsv

SNPs that are part of good quality credible sets as reported in PHENONAME.cred.summary.tsv file.

Column	Description
trait	Phenotype
region	Region for which the fine-mapping was run
v	Variant ID (chr:pos:ref:alt)
cs	Running credible set ID within region
cs_specific_prob	Posterior inclusion probability for this CS
chromosome	Chromosome no.
position	Position on the chromosome
allele1	Major allele
allele2	Minor allele
maf	Minor allele frequency
beta	Original association beta
p	Original p-value
se	Original standard error
most_severe	Most severe consequence of the variant
gene_most_severe	Gene corresponding to most severe consequence

FINEMAP outputs

PHENONAME.FINEMAP.config.bgz

Summary of fine-mapping variant configurations from the FINEMAP method.

Column	Description
trait	Phenotype
region	Region for which the fine-mapping was run
rank	Rank of this configuration within a region
config	Causal variants in this configuration
prob	Probability across all n independent signal configurations
log10bf	Log10 Bayes factor for this configuration
odds	Odds for this configuration
k	How many independent signals are in this configuration
prob_norm_k	Probability of this configuration within k independent signals solution
h2	SNP heritability of this solution
#NAME?	95% confidence interval limits of SNP heritability of this solution
mean	Marginalized shrinkage estimates of the posterior effect size mean
sd	marginalized shrinkage estimates of the posterior effect standard deviation

PHENONAME.FINEMAP.region.bgz

Summary statistics on the number of independent signals in each region.

Column	Description
trait	Phenotype
region	Region for which the fine-mapping was run
h2g_snp or h2g	SNP heritability of this region
h2g_sd	Standard deviation of SNP heritability of this region
h2g_lower95	Lower limit of 95% CI for SNP heritability
h2g_upper95	Upper limit of 95% CI for SNP heritability
log10bf	Log10 Bayes factor compared against null (no signals in the region)
prob_xSNP	x columns for probabilities of different numbers of independent signals
expectedvalue	Expectation (average) of the number of signals

PHENOTYPE.FINEMAP.snp.bgz

Summary statistics of variants and what credible set they are most likely to belong to.

Column	Description
trait	Phenotype
region	Region for which the fine-mapping was run
v	Variant
index	Running index
rsid	Variant ID
chromosome	Chromosome no.
position	Position on the chromosome
allele1	Major allele
allele2	Minor allele
maf	Minor allele frequency
beta	Original marginal beta (effect size)
se	Original standard error
z	Original z-score
prob	Posterior inclusion probability
log10bf	Log10 Bayes factor
mean	Marginalized shrinkage estimates of the posterior effect size mean
sd	Marginalized shrinkage estimates of the posterior effect standard deviation
mean_incl	Conditional estimates of the posterior effect size mean
sd_incl	Conditional estimates of the posterior effect size standard deviation
p	Original p-value
csx	Credible set index for given number of causal variants x

Read more about Finemapping