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: .. image:: images/fullPipeline_output.png :width: 1000 :align: center 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: .. image:: images/grmOnly_output.png :width: 1000 :align: center What can be reused? .. image:: images/grmOnly_output_results_nextSteps.png :width: 1000 :align: center Null Model only ^^^^^^^^^^^^^^^^ Setting this logic: :: GenerateGRM:false GenerateNull:true GenerateAssociations:false GenerateResults:false SkipChunking:false Returns this output: .. image:: images/nullOnly_output.png :width: 1000 :align: center What can be reused? .. image:: images/nullOnly_output_results_nextSteps.png :width: 1000 :align: center Association Analysis only ^^^^^^^^^^^^^^^^^^^^^^^^^ Setting this logic (see :ref:`Option_A`): :: GenerateGRM:false GenerateNull:false GenerateAssociations:true GenerateResults:false SkipChunking:false SaveChunks:true Returns this output: What can be reused? Setting this logic (see :ref:`Option_B`): :: 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 :code:`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 :code:`_commonSNPs_cleaned.txt.gz` and :code:`_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 ===================== ===================================================================================