Hi team

I'm calling somatic variants from FFPE and PBMC paired samples.

I'm wondering is there any sample order preferences in Mutect2 output (such as alphenumeric order).

The tumor/normal order is not always the same (please see my log)

REQUIRED for all errors and issues:
a) GATK version used:

The Genome Analysis Toolkit (GATK) v4.2.0.0
HTSJDK Version: 2.24.0
Picard Version: 2.25.0

 
b) Exact command used:

c) Entire program log:
No software error log

Case 1. Normal sample name preceeds the tumow sample name

##contig=<ID=HLA-DRB1*15:01:01:04,length=11056>
##contig=<ID=HLA-DRB1*15:02:01,length=10313>
##contig=<ID=HLA-DRB1*15:03:01:01,length=11567>
##contig=<ID=HLA-DRB1*15:03:01:02,length=11569>
##contig=<ID=HLA-DRB1*16:02:01,length=11005>
##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##normal_sample=ALD942_Test
##source=Mutect2
##tumor_sample=ALD949
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    ALD942_Test    ALD949

Case 2. Tumor sample is followed by normal sample name

##contig=<ID=HLA-DRB1*15:01:01:04,length=11056>
##contig=<ID=HLA-DRB1*15:02:01,length=10313>
##contig=<ID=HLA-DRB1*15:03:01:01,length=11567>
##contig=<ID=HLA-DRB1*15:03:01:02,length=11569>
##contig=<ID=HLA-DRB1*16:02:01,length=11005>
##filtering_status=Warning: unfiltered Mutect 2 calls.  Please run FilterMutectCalls to remove false positives.
##normal_sample=ALD948_Test
##source=Mutect2
##tumor_sample=ALD936_Test
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    ALD936_Test    ALD948_Test