Dear GATK,

I am using GATK Mutect2  (Gatk4) for variant calling having files with reference hg19. After reading extensively about this topic I understood that b37 is equivalente to hg19 thereby using GERM and PON relative to b37. Yet these files are not compatible with hg19.fa.

export GENOME="/PATH/Manuel/FILES/HUMAN_REFERENCES/hg19.fa"
export GERM="/PATH/Manuel/FILES/HUMAN_REFERENCES/af-only- 
gnomad.raw.sites.vcf"
export PON="/PATH/Manuel/FILES/HUMAN_REFERENCES/Mutect2-WGS- 
panel-b37.vcf"
export VCF="${RECALIBRATED%.bam}.vcf"
srun /mnt/beegfs/apptainer/images/gatk4.sif gatk Mutect2 \
-R $GENOME \
-I $RECALIBRATED \
--germline-resource $GERM \
--panel-of-normals $PON \
-O $VCF

Resulting in the error displayed bellow: 

 A USER ERROR has occurred: Input files reference and features have incompatible contigs: No 
  overlapping contigs found.
  reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr10, chr11, chr12, chr13, 
  chr14, chr15, chr16, chr17, chr18, chr20, chrY, chr19, chr22, chr21, chr6_ssto_hap7, chr6_mcf_hap5, 
  chr6_cox_hap2, chr6_mann_hap4, chr6_apd_hap1, chr6_qbl_hap6, chr6_dbb_hap3, chr17_ctg5_hap1, 
  chr4_ctg9_hap1, chr1_gl000192_random, chrUn_gl000225, chr4_gl000194_random, 
  chr4_gl000193_random, chr9_gl000200_random, chrUn_gl000222, chrUn_gl000212, 
  chr7_gl000195_random, chrUn_gl000223, chrUn_gl000224, chrUn_gl000219, chr17_gl000205_random, 
  chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chr9_gl000199_random, chrUn_gl000211, 
  chrUn_gl000213, chrUn_gl000220, chrUn_gl000218, chr19_gl000209_random, chrUn_gl000221, 
  chrUn_gl000214, chrUn_gl000228, chrUn_gl000227, chr1_gl000191_random, chr19_gl000208_random, 
  chr9_gl000198_random, chr17_gl000204_random, chrUn_gl000233, chrUn_gl000237, chrUn_gl000230, 
  chrUn_gl000242, chrUn_gl000243, chrUn_gl000241, chrUn_gl000236, chrUn_gl000240, 
  chr17_gl000206_random, chrUn_gl000232, chrUn_gl000234, chr11_gl000202_random, chrUn_gl000238, 
 chrUn_gl000244, chrUn_gl000248, chr8_gl000196_random, chrUn_gl000249, chrUn_gl000246, 
  chr17_gl000203_random, chr8_gl000197_random, chrUn_gl000245, chrUn_gl000247, 
   chr9_gl000201_random, chrUn_gl000235, chrUn_gl000239, chr21_gl000210_random, chrUn_gl000231, 
  chrUn_gl000229, chrM, chrUn_gl000226, chr18_gl000207_random]
  features contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, 
  GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, 
  GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, 
  GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1,  
  GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, 
  GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, 
  GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, 
   GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, 
   GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, 
    GL000194.1, GL000225.1, GL000192.1, NC_007605]

This error can be fixed partially by renaming the contigs from 1,2,3,... to chr1,chr2,... . However both lists have different sizes so the mapping is not 1 to 1. 

I know this is debatable topic, but is there any other reference for GERM and PON for hg19 and not b37 that I can use (searched extensively over several resource bundles)?

What would the GATK team recommend doing in this case given that I cannot change the reference, due to the fact that I am starting from sorted.bam files?

Best regards, Manuel Sokolov Ravasqueira