SEQC2 test fails for rtgtools as malformatted INFO field in the truth

Description of the bug

test with SEQC2:

truth_vcf : https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/v1.2.1/sSNV.MSDUKT.superSet.v1.2.vcf.gz

RTGtools error
Command error:
Reference sequence chrY is used in calls but not in baseline.
VCF header does not contain a FORMAT field named GQ
Error: Invalid VCF record. Duplicate INFO field: bwaDP on line:chr2 64622767 . G C . LowConf bwa_PASS=0,0,0,0,0;bowtie_PASS=0,0,0,0,0;novo_PASS=0,0,0,0,0;bwa_REJECT=.;bowtie_REJECT=.;novo_REJECT=.;bwaMQ0=0;bowtieMQ0=0;novoMQ0=0;MQ0=0;bwaTVAF=0.056;bowtieTVAF=0.054;novoTVAF=0.05;TVAF=0.053;bwaNVAF=0;bowtieNVAF=0;novoNVAF=0;NVAF=0;nPASSES=0;nREJECTS=.;bwaDP=48,898;bowtieDP=45,900;novoDP=41,892;FLAGS=Discovered_in_1300X;bwaDP=37,665;bowtieDP=36,668;novoDP=33,661;TVAF95=0.044,0.064;NVAF95=0,0.0011;LC=13.7;PACB_T_DP4=15,12,2,0;PACB_N_DP4=27,25,0,0;PACB_T_DP=2,35;PACB_N_DP=0,55;PACB_TVAF=0.0571;PACB_NVAF=0;PACB_N_MQ=60,.;PACB_T_MQ=60,60 GT:CD4:DP4:MQ0:MSDUKT:NUM_TOOLS:SCORE:VAF:altBQ:altMQ:altNM:fetCD:fetSB:refBQ:refMQ:refNM:zBQ:zMQ 0/0:34,0,3,0:17,17,0,3:0:.:0:.:0.0811:41:60:2:1:0.234:39.5:60:0.0294:0.668:0

Command used and terminal output

Relevant files

No response

System information

No response

Start by downloading the SEQC2 truth VCF from the URL in the report and reproduce the RTGtools validation error, focusing on the duplicate bwaDP INFO field. Then inspect the variantbenchmarking workflow to determine how this truth file is handled; the work is complete when the SEQC2 test has a defined, reproducible outcome without the reported malformed-INFO failure.