Alternative Running Modes

Multiple alternative running modes are enabled with ACEseq.

Run With “Fake” Control

We often observed extremely noisy coverage profiles in matched controls from projects outside the ICGC MMML-Seq, possibly due to wrong handling of blood samples, preventing accurate copy number calls based on tumor/control ratios. For such samples ACEseq offers an option to replace the coverage signal from the matched control with an independent control whilst still maintaining the BAFs of the matched control. This control replacement option enables full analysis of these sample pairs including reliable discrimination between runs of homozygosity (ROH) in the germline and somatic loss of heterozygosity (LOH). Furthermore ACEseq can be run without matched control enlarging the spectrum of samples that can be processed.

To run the workflow in this mode, the runWithFakeControl option should be set to “true”.

<cvalue name="runWithFakeControl" value="true" type="boolean/>
<cvalue name='MALE_FAKE_CONTROL_PRE' value="pathToPID/${pid}/ACEseq/cnv_snp/${pid}.chr" type='path'
        description="path and prefix to chromosome-wise 1kb coverage file used for fake control workflow for male patients" />
<cvalue name='FEMALE_FAKE_CONTROL_PRE' value="pathToPID/${pid}/ACEseq/cnv_snp/${pid}.chr" type='path'
        description="path and prefix to chromosome-wise 1kb coverage file used for fake control workflow for female patients" />
<cvalue name='FAKE_CONTROL_POST' value=".cnv.anno.tab.gz" type='string'
        description="suffix for chromosome wise 1kb coverage files used for fake control workflow"/>

The fake control files should thus be located at ${*_FAKE_CONTROL_PRE}${chromosome}${FAKE_CONTROL_POST}. Each file should be a gzip-compressed TSV with a commented (#) header:

#chr    pos     end     normal  tumor   map

Of these columns the chr and pos columns are used to combine the analysis results of the tumor with the “fake” control file. The normal value from the “fake” control is inserted into the tumor results file (see resources/analysisTools/copyNumberEstimationWorkflow/replaceControlACEseq.R).

If you are operating at the DKFZ you will find a path prefix to a suitable generic control in the default configuration of the workflow.

Run Without Control

If no control sample is available, but ACEseq was already used to process other tumor sample pairs, one of their control coverage profiles can be used for normalization. In this case, no BAFs can be used from a matching control sample and also the patient’s sex is not inferred.

For the configuration you need to specify the path and prefix to a control coverage profile for a male and a female patient so it can be matched to the processed sample. To activate this option the configuration value runWithoutControl (for versions < 3) or isNoControlWorkflow (for versions >= 3) needs to be set to ‘true’, either via the command line execution under cvalues or in the project.xml. Furthermore, the patient’s sex needs to be set explicitly with PATIENTSEX="male|female|klinefelter".

<cvalue name="isNoControlWorkflow" value="true" type="boolean
        description="since version 3"/>
<cvalue name="runWithoutControl" value="true" type="boolean"
        description="up to and including version 2; better use a more recent version!"/>
<cvalue name="PATIENTSEX" value="male|female|klinefelter" />
<cvalue name='MALE_FAKE_CONTROL_PRE' value="pathToPID/${pid}/ACEseq/cnv_snp/${pid}.chr" type='path'
        description="path and prefix to chromosome-wise 1kb coverage file used for fake control workflow for male patients" />
<cvalue name='FEMALE_FAKE_CONTROL_PRE' value="pathToPID/${pid}/ACEseq/cnv_snp/${pid}.chr" type='path'
        description="path and prefix to chromosome-wise 1kb coverage file used for fake control workflow for female patients" />
<cvalue name='FAKE_CONTROL_POST' value=".cnv.anno.tab.gz" type='string'
        description="suffix for chromosome wise 1kb coverage files used for fake control workflow"/>

Note that if run in no-control mode with SV input (you have svOutputDirectory set), then ACEseq does not expect the SV file to be named svs_${PID}_filtered_somatic_minEventScore3.tsv, like for the tumor/control case, but svs_${PID}_filtered_minEventScore3.tsv. If you use an output directory of the Sophia workflow in no-control mode, you can simply symlink the svs_${PID}_filtered_minEventScore3.tsv to create the “somatic”.

Run quality check only

In case you do not want to run the full ACEseq pipeline immediately, but would rather access the sample’s quality first you can start ACEseq with the option “runQualityCheckOnly” set to “true”.

Replace low quality control

If a control sample is very noisy and masks CNAs it can be replaced with the coverage profile from a different control of the same sex. For this run ACEseq with “runWithFakeControl” set to “true” and specify the values “FEMALE_FAKE_CONTROL_PRE” and “MALE_FAKE_CONTROL_PRE” as described in the section for analysis without matched control.

Run with/without SV breakpoint incorporation

To process samples with incorporation of SV breakpoints set the following in the project.xml:

<configurationvalues>
  <cvalue name='svOutputDirectory' value='${outputAnalysisBaseDirectory}/nameOfDirectoryWithSVResults' type="path"/>
  <cvalue name='runWithSv' value='true' type="boolean"/>
</configurationvalues>

<filenames package='de.dkfz.b080.co.files' filestagesbase='de.dkfz.b080.co.files.COFileStage'>
      <filename class="TextFile" onMethod="de.dkfz.b080.co.aceseq.ACESeqMethods.mergeSv"
                selectiontag="svFileTag"
                pattern='${svOutputDirectory}/${pid}_svs.bedpe'/>
</filenames>

If the bedpe file does not exist ACEseq will submit all steps until the bedpe file is required. A rerun once the SV file is generated will start the pipeline up from the point where SV breakpoints are incorporated.

To process a samples without SVs please set the following in the project.xml:

<cvalue name='runWithSv' value='false' type="boolean"/>
<cvalue name='SV' value='no' type="string"/>