HaplotypeCaller should not write command line parameters in result file
Description (last modified by )
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)