The current GATK version is 3.2-2

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Posts: 85Member ✭✭✭

I'm wondering if there's any way to skip the GATKCommandLine line in the vcf-header (in a vcf file generated by UnifiedGenotyper). I thought that the --remove_program_records would do this but it doesn't seem to do the trick. I'm still seeing the header line.

##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-2-g6bda569,Date="Fri Sep 27 15:17:59 CEST 2013", [...] >

The reason this is important to me is that I'm using the Pipeline test code provided in Queue and, as you know, this is based on md5 sums, and as the time when the tests was run is included, the md5 hash changes for each run. So, if there is no way to skip the header, is there any other, better way to do this.

Cheers, Johan

Tagged:

The --no_cmdline_in_header argument should do what you want.