Opened 8 months ago

Closed 8 months ago

#1082 closed enhancement (fixed)

HaplotypeCaller should not write command line parameters in result file

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: Reggie v4.21
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

Just in case the command line contains some sensitive information. HaplotypeCaller is currently used in two places:

  • During Hisat alignment to generate a VCF file for QC checks
  • In the mBAF analysis step to generate a VCF file for calculating mBAF

Both of those steps seems to be fine with respect to sensitive information and there is no need to fix the existing VCF files.

Existing VCF files can easily be fixed by searching for a line starting with ##GATKCommandLine (it should be near the top of the file) and remove it.

The output of the command line parameters should be prevented by adding --no_cmdline_in_header to the command line (see https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_engine_CommandLineGATK.php)

Change History (2)

comment:1 Changed 8 months ago by Nicklas Nordborg

Description: modified (diff)

comment:2 Changed 8 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

(In [5118]) Fixes #1082: HaplotypeCaller? should not write command line parameters in result file

Added to the configuration file and also in the code to make sure that it is always set.

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