In GATK3, using multiple bams in the -I parameter would print multiple columns of genotypes. This doesnt seem to happen with GATK4. Here is the command
gatk --java-options "-Xmx60G" HaplotypeCaller \
-I $BAM1 \
-I $BAM2 \
--genotyping-mode DISCOVERY \
-R $ref \
-D $dbsnp \
-O $out_directory$fname.el.snps.vcf
Here is the output
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --dbsnp /home/exacloud/tempwork/SpellmanLab/heskett/DBSNP_150_uw.vcf --genotyping-mode DISCOVERY --output 4e700.sorted.de-duplicated.recalibrated.el.snps.vcf --input 4e700.sorted.de-duplicated.recalibrate
d.bam --input 4l700.sorted.de-duplicated.recalibrated.bam --reference /home/exacloud/lustre1/SpellmanLab/heskett/refs/myron_refs/human_g1k_v37.fasta
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1
1 12783 rs62635284 G A 251.77 . AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.24;QD=25.18;SOR=4.804 GT:AD:DP:GQ:PL 1/1:0,10:10:30:280,30,0
1 13116 rs62635286 T G 710.77 . AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.05;QD=25.36;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,17:17:51:739,51,0
1 13118 rs62028691 A G 710.77 . AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.73;QD=28.73;SOR=0.818 GT:AD:DP:GQ:PL 1/1:0,15:15:51:739,51,0
is this feature not implemented yet? or did the command line call change?
Thanks!