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problems emitting all sites with HaplotypeCaller
I'm running GATK v18.104.22.168 and Java v1.8.0_20
I'd like to get a VCF with all callable positions, including invariants. With GATK 3, using UnifiedGenotyper, this process works great. I'm trying to run with GATK 4 and I'm only getting the variant positions. Here is my command:
gatk HaplotypeCaller -R reference.fasta -I ECOLI_renamed_header.bam -O test.vcf --output-mode EMIT_ALL_SITES
The VCF only contains one position:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test
ADK1 460 . A G 81.28 . AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.09;SOR=2.833 GT:AD:DP:GQ:PL 1/1:0,3:3:9:109,9,0
When I run a comparable command with GATK 3, I get 536 positions reported, with only one of them being a variant.
Am I running this correctly?