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MuTect2 output shows the sample name as "$sp" instead of "TUMOR" and "NORMAL"

Here is my code:

java -jar GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar \
-T MuTect2 -L chrM -I:tumor Exon_P3_TXC_PT1.realn_Recal.bam \
-I:normal Exon_P3_TXC_N/Exon_P3_TXC_N.realn_Recal.bam \
--dbsnp dbsnp_135.hg19.vcf --output_mode EMIT_VARIANTS_ONLY -o test.vcf.gz -R genome.fa

The output shows that the sample name is "$sp" instead of "TUMOR" and "NORMAL".
Here is the output file (test.vcf.gz):

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT $sp
chrM 3395 . T C . alt_allele_in_normal;clustered_events;t_lod_fstar ECNT=3;HCNT=13;MAX_ED=27;MIN_ED=1;NLOD=34.28;TLOD=4.37 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1 0/0:147,3:0.020:1:2:0.333:0|1:3395_T_C:4031,59:72:75
chrM 3396 . A G . alt_allele_in_normal;clustered_events;t_lod_fstar ECNT=3;HCNT=13;MAX_ED=27;MIN_ED=1;NLOD=33.98;TLOD=4.38 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1 0/0:148,3:0.021:1:2:0.667:0|1:3395_T_C:3715,61:72:76
chrM 3422 . G A . alt_allele_in_normal;clustered_events ECNT=3;HCNT=16;MAX_ED=27;MIN_ED=1;NLOD=9.29;TLOD=19.31 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:154,12:0.077:7:5:0.583:4237,317:76:78
chrM 3698 . G T . alt_allele_in_normal;t_lod_fstar ECNT=1;HCNT=21;MAX_ED=.;MIN_ED=.;NLOD=39.42;TLOD=6.27 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:197,5:0.027:4:1:0.800:5645,138:93:104
chrM 13189 . C A . alt_allele_in_normal;t_lod_fstar ECNT=1;HCNT=36;MAX_ED=.;MIN_ED=.;NLOD=27.20;TLOD=4.07 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:139,6:0.038:3:3:0.500:4167,133:72:67
chrM 14784 . T C . alt_allele_in_normal ECNT=1;HCNT=40;MAX_ED=.;MIN_ED=.;NLOD=11.41;TLOD=9.65 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:102,8:0.067:5:3:0.625:2854,188:60:42

Answers

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