Options

The options for Reference population genotypes, GWAS summary statistics, and Global misc act on all the analyses. For clarity, we have categorized the other parameters by GATES and EHE, DESE, EMIC and EHE, although this has resulted in duplications.

In the “Default” columns of the following tables, “null” denotes that the flag works with an argument but there is no default value; “n/a” denotes that the flag works without any argument.

Reference population genotypes

These options work on the VCF file of reference population genotypes. Only SNPs that pass the filters will be used for subsequent analyses.

Flag	Description	Default
--vcf-ref	Specifies a VCF file of genotypes sampled from the target population. These genotypes are used to estimate LD correlation coefficients between any pair of SNPs. For VCF files of separated chromosomes, use wildcards and quotes like "chr*.vcf.gz".	null
--keep-ref	Specifies a directory to keep the parsed VCF files in KGGSEE object format.	null
--saved-ref	Specifies the directory of the genotypes of the reference population in KGGSEE object format, which was saved by --keep-ref. Reading KGGSEE object format files is faster than parsing VCF files.	null
--filter-maf-le	Filter SNPs with a minor allele frequency lower than the setting.	0.05
--hwe-all	Filter SNPs with a p-value of rejecting Hardy-Weinberg equilibrium lower than the setting.	1E-5
--chrom	Specify chromosome labels. e.g., --chrom NC_052532.1,NW_024095932.1,NW_024095933.1,NW_024095934.1.	1,…,22,X,Y,M
--ld-block-max-r2	Set the max tolerable LD coefficient between SNPs from two LD blocks. KGGSEE divides SNPs within a genomic region into LD blocks to improve computational efficiency. Any pairwise LD coefficient between SNPs from two LD blocks are always less than the number specified by --ld-block-max-r2. A smaller number leads to larger LD blocks and in turn more RAM and CPU time usage; a larger number may increase the sampling error of LD coefficient estimates. We recommand that only increase the number when the partitioned LD blocks are too big to be analyzed.	0.15
ld-block-win	Set the window size in base-pair for searching LD blocks on chromosomes	5000000

GWAS summary statistics

Flag	Description	Default
--sum-file	Specifies a whitespace delimitated file of GWAS summary statistics.	null
--chrom-col	Specifies the column header of chromosomes.	CHR
--pos-col	Specifies the column header of coordinates.	BP
--p-col	Specifies the column header of p-values.	P
--a1-col	Specifies the column header of the effect allele.	A1
--a2-col	Specifies the column header of the other allele.	A2
--freq-a1-col	Specifies the column header of the frequencies of the allele specified by --a1-col.	FRQ_U
--beta-col	Specifies the column header of effect sizes.	null
--beta-type	Specifies the type of effect sizes: 0 for the linear regression coefficient of a quantitative trait; 1 for the logarithm of odds ratio or logistic regression coefficient of a dichotomous trait; 2 for an odds ratio of a dichotomous trait.	null
--se-col	Specifies the column header of standard errors of effect sizes. Note: even if the effect size is provided as an odds ratio, this is still the standard error of the logarithm (base e) of the odds ratio.	SE
--nmiss-col	Specifies the column header of sample sizes for a quantitative trait.	null
--case-col	Specifies the column header of case sample sizes for a qualitative trait.	null
--control-col	Specifies the column header of control sample sizes for a dichotomous trait.	null
--adjust-gc	Ask KGGSEE to adjust the p-values and chi-square statistics using the genomic control factors from the input GWAS data before all follow-up analyses.	1

Global misc

Flag	Description	Default
--nt	Specifies the number of threads.	4
--lib-update	Download kggsee.jar from http://pmglab.top/kggsee and replace the current running one.	n/a
--buildver	Specifies the reference genome version of the coordinates. The supported versions are hg19 and hg38.	hg19
--db-gene	Specifies the database of gene annotations. refgene for RefSeq Genes; gencode for GENCODE; refgene,gencode for both.	refgene
--excel	Output results in Excel format.	n/a
--only-hgnc-gene	Only genes with an HGNC-approved gene symbol are considered in the analysis.	n/a
--out	Specifies the output prefix of results.	./kggsee1
--regions-bed	Specify a BED file to define customized gene coordinates instead of the annotation from RefSeqGene or GENCODE. The first three columns of the BED file define gene coordinates and are mandatory; the fourth column defines gene names and is optional. When the fourth column is absent, a gene name of the format like chr1:100-200 will be allocated.	null
--regions-out	Specifies genomic regions to be excluded in the analysis, e.g., chr1,chr2:2323-34434,chr2:43455-345555.	null
--resource	Specifies the path KGGSEE running resource data.	path/to/kggsee.jar/resources/

GATES and ECS

Flag	Description	Default
--gene-assoc	Triggers gene-based association tests.	n/a
--neargene	One number sets the basepair to extend at both sides of a gene, when considering SNPs belonging to the gene, e.g., --neargene 5000. This flag can also have two values to set an asymmetric boundary extension, e.g., 5 kb upstream and 15 kb downstream of a gene can be set by --neargene 5000,15000.	5000
--eqtl-file	Specifies a fasta-styled file of eQTL summary statistics. If this flag is used, --neargene is overridden, and eQTLs of a gene or transcript will be grouped and tested.	null
--filter-eqtl-p	Specifies the threshold of eQTL p-values. Only eQTLs with a p-value lower than the threshold will be used. The default is 0.01 when performing gene-based association tests and heritability estimation.	0.01

DESE

Flag	Description	Default
--gene-assoc-condi	Trigers the DESE, eDESE or SelDP.	n/a
--expression-file	Specifies a gene expression file that contains means and standard errors of gene expressions in multiple tissues.	null
--multiple-testing	Specifies the method for multiple testing correction. bonf denotes performing Bonferroni correction; benfdr denotes controlling false discovery rate by the Benjamini–Hochberg method; fixed denotes no correction.	bonf
--p-value-cutoff	Specifies the threshold of the adjusted p-value for fine-mapping. Only genes with an adjusted p-value lower than the threshold will be retained for fine-mapping.	0.05
--top-gene	Specifies the maximum number of genes with the smallest p-values that will be retained for fine-mapping.	null
--geneset-db	Specifies MSigDB gene sets for enrichment analysis: cura: C2. curated gene sets; cgp: C2. chemical and genetic perturbations; cano: C2. canonical pathways; cmop: C4. computational gene sets; onto: C5. ontology gene sets; onco: C6. oncogenic signature gene sets; immu: C7. immunologic signature gene sets.	null
--geneset-file	Specifies a user-defined file of gene sets for enrichment analysis.	null
--neargene	One number sets the basepair to extend at both sides of a gene when considering SNPs belonging to the gene, e.g., --neargene 5000. This flag can also have two values to set an asymmetric boundary extension, e.g., 5 kb upstream and 15 kb downstream of a gene can be set by --neargene 5000,15000.	5000
--eqtl-file	Specifies a fasta-styled file of eQTL summary statistics. If this flag is used, --neargene is overridden, and eQTLs of a gene or transcript will be grouped and tested.	null
--filter-eqtl-p	Specifies the threshold of eQTL p-values. Only eQTLs with a p-value lower than the threshold will be used. The default is 0.01 when performing DESE.	0.01
--dese-permu-num	The number of permutations for an adjustment of selection bias and multiple testing	null

EMIC

Flag	Description	Default
--emic	Triggers the EMIC.	n/a
--eqtl-file	Specifies a fasta-styled file of eQTL summary statistics.	null
--filter-eqtl-p	Specifies the threshold of eQTL p-values. Only eQTLs with a p-value lower than the threshold will be used. The default is 1E-4 when performing EMIC.	1E-4
--ld-pruning-mr	Specifies the threshold of LD coefficients when pruning variants. For each gene or transcript, eQTLs with LD coefficients higher than the threshold will be pruned.	0.5
--emic-pfm-p	Specifies the p-value threshold to further perform an EMIC pleiotropy fine-mapping (EMIC-PFM) analysis. If the EMIC p-value of a gene is lower than the threshold, an EMIC-PFM will be performed to control the false-positive caused by pleiotropy.	2.5E-6
--emic-plot-p	Specifies the p-value threshold for plotting a scatter plot. Genes with an EMIC p-value lower than the threshold will be plotted.	2.5E-3

EHE

Flag	Description	Default
--gene-herit	Triggers gene-based association tests and estimation of gene heritability. The flags of --neargene, --eqtl-file and --filter-eqtl-p have the same meaning as in GATES and ECS.	n/a
--case-col, --control-col, --nmiss-col	When --case-col and --control-col are specified, KGGSEE will regard the input as summary statistics from case/control samples and automatically adjust for the disease prevalence. On the other hand, if the --nmiss-col is specified, KGGSEE will regard the input as summary statistics for a quantitative trait.	null
--gene-assoc-condi	When --gene-assoc-condi is specified in addition to --gene-herit, KGGSEE also calculates the conditional heritability, and the flags of --multiple-testing, --p-value-cutoff, --top-gene and --expression-file have the same meaning as in DESE.	n/a
--prevalence	Specifies the proportion of cases in the population when estimating the heritability of a dichotomous trait.	0.01