Hello there,

I used to run the following command, to merge VCF from 2 callers (freebayes et GATK);
infos fields were first preceded by a unique tag, both in the headers and in each record, to be sure they won't be merged during the process.

java -Xmx8g -jar path/GenomeAnalysisTK.jar -T CombineVariants -R genome.fasta -dt NONE --filteredrecordsmergetype KEEP_UNCONDITIONAL -V path/sample.freeb.toolInfo.vcf -V path/sample.gatk.toolInfo.vcf -o path/sample1.mergeTool.vcf

with GATK 3.7 or 3.8, I got:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT freeb_6991_S1 gatk_6991_S1

chr1 1915326 rs2247560 G A 44833.90 PASS AC=2;AC_Orig=9;AF=0.500;AN=4;AN_Orig=16;HET;SNP;VARTYPE=SNP;gatk_DB;set=FilteredInAll GT:AD:AO:DP:GQ:PL:QA:QR:RO 0/1:158,200:200:358:.:4882,0,3530:6621:5118:158 0/1:152,194:.:346:99:4811,0,3343

with GATK3.5 or 6, I got the full infos:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT freeb_6991_S1 gatk_6991_S1

chr1 1915326 rs2247560 G A 44833.90 PASS AC=2;AC_Orig=9;AF=0.500;AN=4;AN_Orig=16;HET;SNP;VARTYPE=SNP;freeb_AB=0.52806;freeb_ABP=15.8059;freeb_AC=1;freeb_AF=0.5;freeb_AN=2;freeb_AO=1747;freeb_CIGAR=1X;freeb_DP=358;freeb_DPB=3033;freeb_DPRA=0.934968;freeb_EPP=59.4027;freeb_EPPR=57.3242;freeb_FILTER=run_hetF0.2;freeb_FOUND=1;freeb_GTI=0;freeb_LEN=1;freeb_MEANALT=1.42857;freeb_MQM=60;freeb_MQMR=60;freeb_NS=8;freeb_NUMALT=1;freeb_ODDS=276.245;freeb_PAIRED=0.995993;freeb_PAIREDR=0.996877;freeb_PAO=0;freeb_PQA=0;freeb_PQR=0;freeb_PRO=0;freeb_QA=56376;freeb_QR=41649;freeb_QUAL=44833.9;freeb_RO=1281;freeb_RPL=940;freeb_RPP=24.9972;freeb_RPPR=41.6612;freeb_RPR=807;freeb_RUN=1;freeb_SAF=811;freeb_SAP=22.4317;freeb_SAR=936;freeb_SRF=597;freeb_SRP=15.8408;freeb_SRR=684;freeb_TYPE=snp;freeb_meanARF=0.58;freeb_medARF=0.26;freeb_minARF=0;freeb_run_AC=9;freeb_run_AF=0.5625;freeb_run_AN=16;freeb_run_hetC=5;freeb_run_hetF=0.625;freeb_run_homC=2;freeb_run_homF=0.25;freeb_run_sampleC=7;freeb_run_sampleF=0.875;freeb_stdARF=0-1.174;freeb_technology.ILLUMINA=1;gatk_AC=1;gatk_AF=0.5;gatk_AN=2;gatk_BaseQRankSum=0.071;gatk_ClippingRankSum=0;gatk_DB;gatk_DP=346;gatk_ExcessHet=4.8882;gatk_FILTER=run_hetF0.2;gatk_FOUND=1;gatk_FS=0.559;gatk_MQ=60;gatk_MQRankSum=0;gatk_QD=17.54;gatk_QUAL=44588.8;gatk_ReadPosRankSum=0.737;gatk_SOR=0.759;gatk_meanARF=0.585;gatk_medARF=0.78;gatk_minARF=0;gatk_run_AC=9;gatk_run_AF=0.5625;gatk_run_AN=16;gatk_run_hetC=5;gatk_run_hetF=0.625;gatk_run_homC=2;gatk_run_homF=0.25;gatk_run_sampleC=7;gatk_run_sampleF=0.875;gatk_stdARF=0-1.177;set=FilteredInAll GT:AD:AO:DP:GQ:PL:QA:QR:RO 0/1:158,200:200:358:.:4882,0,3530:6621:5118:158 0/1:152,194:.:346:99:4811,0,3343

did I missed an option?

many thanks in advance

thomas