Output Generated

This summarizes the expected output depending on how the pipeline logic boolean values are set in the config file.

Full Pipeline with Chunking

Setting this logic:

GenerateGRM:true
GenerateNull:true
GenerateAssociations:true
GenerateResults:true
SkipChunking:false
SaveChunks:true

Returns this output:

What can be reused?

Genetic Relatedness Matrix (GRM) only

Setting this logic:

GenerateGRM:true
GenerateNull:false
GenerateAssociations:false
GenerateResults:false
SkipChunking:false

Returns this output:

What can be reused?

Null Model only

Setting this logic:

GenerateGRM:false
GenerateNull:true
GenerateAssociations:false
GenerateResults:false
SkipChunking:false

Returns this output:

What can be reused?

Association Analysis only

Setting this logic (see OPTION A: Imputation files need window chunking):

GenerateGRM:false
GenerateNull:false
GenerateAssociations:true
GenerateResults:false
SkipChunking:false
SaveChunks:true

Returns this output:

What can be reused?

Setting this logic (see OPTION B: Imputation files do not need window chunking and will be reused):

GenerateGRM:false
GenerateNull:false
GenerateAssociations:true
GenerateResults:false
SkipChunking:true

Returns this output:

What can be reused?

Output Files Generated

This section describes the file format output and what is located in each result file.

For association analysis results file per snp. This is for text files generated with the suffix: * *_allSNPs_noFiltering.txt.gz * *_commonSNPs_cleaned.txt.gz * *_rareSNPs_cleaned.txt.gz

Column	Interpretation
CHR	chromosome the variant is located
POS	base position of the variant (hg19 vs hg38 is based upon what was specified at runtime)
majorAllele	major allele (most common frequency in the input population)
minorAllele	minor allele (lesser common frequency in the input population)
SNPID	variant name
BETA	effect size based on the minor allele
SE	standard error of beta
OR	odds Ratio
LogOR	log(odds ratio)
Lower95OR	lower 95% confidence interval of the odds ratio
Upper95OR	upper 95% confidence interval of the odds ratio
MAF	minor allele frequency
MAC	minor allele count
p.value	p-value of the variant
N.Cases	number of cases evaluated for this variant (binary traits only)
N.Controls	number of controls evaluated for this variant (binary traits only)
casesHomMinor	number of cases evaluated for this variant that are homozygous for the minor allele (binary traits only)
casesHet	number of cases evaluated for this variant that are heterozygous (binary traits only)
controlHomMinor	number of control evaluated for this variant that are homozygous for the minor allele (binary traits only)
controlHet	number of controls evaluated for this variant that are heterozygous (binary traits only)
negLog10pvalue	negative log base 10 of the p-value
R2	imputation quality for imputed variants
ER2	empirical R2 quality extracted from info file from imputation – for genoytyped variants only
GENOTYPE_STATUS	imputed, genotyped or genotyped and imputed status for the variant

There is an intermediate file also output with the suffix allChromosomeResultsMerged.txt. This is output directly from SAIGE, however, it is not cleaned and alleles and betas have not been corrected for minor allele basis. All GWAS results, including the graphs generated from the pipeline are based on the files above ending in _commonSNPs_cleaned.txt.gz and _rareSNPs_cleaned.txt.gz.

However, some T statistics and variance calculations are included in this file, along if the variant converged or not. Therefore, it is still saved in the output so it can easily be searched and referenced for particular variants, if needed.

Column	Interpretation
CHR	chromosome the variant is located
POS	base position of the variant
SNPID	variant name
Allele1	allele 1 (careful, not necessarily major allele)
Allele2	allele 2 (careful, not necessarily minor allele)
AC_Allele2	allele count of allele 2
AF_Allele2	allele frequency of allele 2 (not necessarily minor allele)
imputationInfo	imputation quality score
N	total samples considered in model for this variant
BETA	effect size of allele 2 (not necessarily minor allele)
SE	standard error of beta
p.value	p-value of the variant
p.value.NA	p-value of variant when SPA is not applied
Is.SPA.converge	whether saddle point approximation (SPA) converged for this variant
Tstat	estimated variance of score statistic with sample related incorporated
varTstar	variance of score statistic without sample related incorporated
AF.Cases	allele frequency of allele 2 in cases (only for binary trait)
AF.Controls	allele frequency of allele 2 in controls (only for binary traits)
N.Cases	total cases considered in model for this variant (only for binary traits)
N.Controls	total controls considered in model for this variant (only for binary traits)
homN_Allele2_cases	homozygote counts in cases
hetN_Allele2_cases	heterozygote counts in cases
homN_Allele2_ctrls	homozygote counts in controls
hetN_Allele2_ctrls	heterozygote counts in controls