Tutorial: Generate Association Analysis Only

This example will show you how to generate the association analysis step only. It will guide you through how to properly set the logic, remind you to set the environment, list all the additional files you need, and finally which user parameters need to be set.

Section: Logic and Overview

Association Analysis only means you only want to run the association anlysis. It makes an assumption that you already have the null model file (.rda) pre-calculated and have a pre-calculate variance ratio file (.varianceRatio.txt) and want to re-use/use it in this step by setting the keywords NullModelFile and VarianceRatioFile located in the config file. These two files are the result of running GenerateNull:true.

Choosing to run just the association analysis step is analagous to setting the pipeline logic kewords to the following:

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

When GenerateAssociations:true, the SkipChunking logic comes into play. This logic parameter depends upon whether you have already chunked the genotype and/or imputation files into windows and saved those from a previous run.

• If you have not chunked or didn’t save them you will set SkipChunking:false. You will be following all the OPTION A: Imputation files need window chunking steps.

• If you have saved chunks, then you can reuse those chunked files and set SkipChunking:true. You will be following all the OPTION B: Imputation files do not need window chunking and will be reused steps.

Warning

This step produces the raw associaions results concatenated into a file. It does not clean up the data, perform the proper flips, or generate graphs/figures. If you want the raw data in addition to the previously mentioned actions, be sure to also set GenerateResults:true.

Section: Step-by-Step Tutorial

OPTION A: Imputation files need window chunking

If the pipeline is set to the above logic with SkipChunking:false, the following workflow will be executed:

(A) STEP 1: Set the logic – if window chunking is needed

As stated about above, open your config file (.txt) and make sure the logic is set to the following:

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

(A) STEP 2: Set the environment

Open your config file (.txt) and make sure you set the path to where the bind point, temp bind point, and container image are located. I suggest you set the BindPoint keyword to the same path as where the container is located to avoid any confusion. If you have a tmp directory you want to use as scratch space, set that path as well. If this doesn’t exist or you choose not to use it, set the keyword BindPointTemp to be the same as the path listed in the keyword BindPoint.

BindPoint:/path/to/bind/container
BindPointTemp:/path/to/tmp/
Container:/path/to/saige-brush-v039.sif

(A) STEP 3: Ensure you have all the files required

For running the null model only, you will need access to the following files:

1. LD-pruned plink file

   • used for when logic parameters GenerateGRM is set to true and/or GenerateNull is set to true and/or GenerateAssociation is set to true.

   • fulfills parameter Plink

   • see Parameter: Plink for formatting

2. phenotype and covariates file

   • used for when logic parameter GenerateNull is set to true and/or GenerateAssociations is set to true.

   • fulfills parameter PhenoFile

   • see Parameter: PhenoFile for formatting

3. chromosome lengths file

   • used for when logic parameter SkipChunking is set to false

   • fulfills parameter ChromosomeLengthFile

   • see Parameter: ChromosomeLengthFile for file formatting

4. imputation files or genotype files in vcf.gz format with .tbi index

   • used for when logic parameter GenerateAssociations is set to true

   • fulfills parameters ImputeDir and ImputeSuffix

   • see Parameter: ImputeSuffix for file input and naming expectations

5. pre-calculated GRM with corresponding sample order file

   • used for when logic parameter GenerateNull is set to true and/or GenerateAssociations is set to true.

   • fulfills parameters SparseGRM and SampleIDFile

   • see Parameter: SparseGRM and Parameter: SampleIDFile for formatting

6. pre-calculated Null model with corresponding variance ratio file

   • used for when logic parameter GenerateAssociations is set to true

   • fulfills parameters NullModelFile and VarianceRatioFile

   • see Parameter: NullModelFile and Parameter: VarianceRatioFile for formatting

Note

Missing the pre-calculated GRM files? No problem. If you set the logic to GenerateGRM:true, one will be calculated for you! Just make sure you also set the GRM parameters you want and set the appropriate paths to the required input files you want. For more information on what parameters you need to fill out, see Minimum requirements for Generating a GRM or look at the GRM only tutorial.

Note

Missing the pre-calculation null model files? No problem. If you set the logic to GenerateNull:true, one will be calculated for you! Just make sure you also set the Null parameters you want and set the appropriate paths to the required input files. For more information on what parameters you need to fill out, see Minimum requirements for Generating a Null Model or look at the Null model only tutorial.

See also

For a complete list of files and name formatting of keyword values listed in the config file see Formatting the Required Files.

(A) STEP 4: Set the path and values to all the required input parameters

Now that you have all the required files, it is time to set the values and locations within your config file using the keywords expected. Here are the required keywords and how to specify them:

1. This RUNTYPE parameter need to just be here for placeholder purposes, however it is required. It has no impact on the pipeline, except as a header to check that it exists.

   RUNTYPE:FULL
   

OPTION B: Imputation files do not need window chunking and will be reused

If the pipeline is set to the above logic with SkipChunking:true, the following workflow will be executed:

(B) STEP 1: Set the logic – if reusing pre-chunked imputation files

As stated about above, open your config file (.txt) and make sure the logic is set to the following:

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

(B) STEP 2: Set the environment

Open your config file (.txt) and make sure you set the path to where the bind point, temp bind point, and container image are located. I suggest you set the BindPoint keyword to the same path as where the container is located to avoid any confusion. If you have a tmp directory you want to use as scratch space, set that path as well. If this doesn’t exist or you choose not to use it, set the keyword BindPointTemp to be the same as the path listed in the keyword BindPoint.

BindPoint:/path/to/bind/container
BindPointTemp:/path/to/tmp/
Container:/path/to/saige-brush-v039.sif

(B) STEP 3: Ensure you have all the files required

For running the null model only, you will need access to the following files:

1. LD-pruned plink file

   • used for when logic parameters GenerateGRM is set to true and/or GenerateNull is set to true and/or GenerateAssociation is set to true.

   • fulfills parameter Plink

   • see Parameter: Plink for formatting

2. phenotype and covariates file

   • used for when logic parameter GenerateNull is set to true and/or GenerateAssociations is set to true.

   • fulfills parameter PhenoFile

   • see Parameter: PhenoFile for formatting

3. imputation files or genotype files in vcf.gz format with .tbi index pre-chunked

   • used for when logic parameter GenerateAssociations is set to true and SkipChunking is set to true.

   • fulfills parameters ImputeDir, ImputeSuffix, and ImputationFileList:

   • when SkipChunking:true, the ImputeDir parameter in the config file should be the directory where all your chunked imputation files are located. The suffix remains the same as the original imputation suffix prior to chunking.

   • see Parameter: ImputeSuffix and Parameter: ImputationFileList for file input and naming expectations

4. pre-calculated GRM with corresponding sample order file

   • used for when logic parameter GenerateNull is set to true and/or GenerateAssociations is set to true.

   • fulfills parameters SparseGRM and SampleIDFile

   • see Parameter: SparseGRM and Parameter: SampleIDFile for formatting

5. pre-calculated Null model with corresponding variance ratio file

   • used for when logic parameter GenerateAssociations is set to true

   • fulfills parameters NullModelFile and VarianceRatioFile

   • see Parameter: NullModelFile and Parameter: VarianceRatioFile for formatting

Note

Missing the pre-calculated GRM files? No problem. If you set the logic to GenerateGRM:true, one will be calculated for you! Just make sure you also set the GRM parameters you want and set the appropriate paths to the required input files you want. For more information on what parameters you need to fill out, see Minimum requirements for Generating a GRM or look at the GRM only tutorial.

Note

Missing the pre-calculation null model files? No problem. If you set the logic to GenerateNull:true, one will be calculated for you! Just make sure you also set the Null parameters you want and set the appropriate paths to the required input files. For more information on what parameters you need to fill out, see Minimum requirements for Generating a Null Model or look at the Null model only tutorial.

See also

For a complete list of files and name formatting of keyword values listed in the config file see Formatting the Required Files.

(B) STEP 4: Set the path and values to all the required input parameters

Now that you have all the required files, it is time to set the values and locations within your config file using the keywords expected. Here are the required keywords and how to specify them:

1. This RUNTYPE parameter need to just be here for placeholder purposes, however it is required. It has no impact on the pipeline, except as a header to check that it exists.

   RUNTYPE:FULL
   

Section: Generated Output

See also

For a interpreting and searching the log files for potential pipeline errors, see Parsing Through StdErr and StdOut.