The  final three lines in the mutect2 header above the column headers is listed as:

##source=Mutect2
##tumor_sample=N31May2020
##tumor_sample=T31May2020

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT N31May2020 T31May2020

For reasons that are not clear they are both labeled 'tumor_sample'?

The sample Id is based on a -SM= in the fastq->BAM process which then has been traversed through the remainder of the 'Best Practices"  .  After alignment, deduping, and base quality recalibration the files were sent to mutect2 and then filtered. 

I presume my -SM= identifiers are correct and therefore that the 'N' sample is column 10 and the 'T' sample is column 11. Is that correct?

If that is the case then the MAF file from Funcotator is using the wrong column.  The "t_alt_count' column data is sourced from the column10 (N31May2020 ) that is derived from the BAM file from my 'N' = normal somatic sample.

How to fix?

two input files arguments are sent in the order to specified in the online info i.e. tumor followed by normal.  

--input tumor.bam

--input normal.bam

Can you please provide
a) GATK version used   'latest' GATK docker versionj
b) Exact GATK commands used
c) The entire error log if applicable.

##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output mydata/P62820/analysis/P62820_mutect2_filtered.vcf --stats mydata/P62820/analysis/P62820_rpt_mutect2_unfiltered.vcf.stats --variant mydata/P62820/analysis/P62820_rpt_mutect2_unfiltered.vcf --reference mydata/refs/Homo_sapiens_assembly19.fasta --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --min-reads-per-strand 0 --min-allele-fraction 0.0 --contamination-estimate 0.0 --log-snv-prior -13.815510557964275 --log-indel-prior -16.11809565095832 --log-artifact-prior -2.302585092994046 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.7.0",Date="June 2, 2020 2:57:05 AM UTC">

##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --output mydata/P62820/analysis/P62820_rpt_mutect2_unfiltered.vcf --intervals mydata/refs/hg19_intervals.interval_list --input mydata/P62820/bsqr/P62820_Tbwa_dedup_bsqr.bam --input mydata/P62820/bsqr/P62820_Nbwa_dedup_bsqr.bam --reference mydata/refs/Homo_sapiens_assembly19.fasta --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.7.0",Date="June 1, 2020 5:25:40 PM UTC">