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

[kubranarci]

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

[kubranarci]

This error does not happen when limit the analysis to high-conf regions: "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/v1.1/High-Confidence_Regions.bed"