Alternative Running Modes

Multiple alternative running modes are enabled with ACEseq.

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 profile can be used for normalization. In this case the patient’s sex needs to be set with PATIENTSEX=”male|female|klinefelter”.

Please specify the path and prefix to a control coverage profile for a male (MALE_FAKE_CONTROL_PRE) and a female patient (FEMALE_FAKE_CONTROL_PRE) so it can be matched to the processed sample. To activate this option the value runWithout control needs to be set to ‘true’, either via the command line execution under cvalues or in the project.xml.

<cvalue name="runWithoutControl" value="true" type="boolean" />
<cvalue name="PATIENTSEX" value="male|female|klinefelter" 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" />

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"/>