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UnifiedGenotyper different results depending on the output mode
I'm using GATK UnifiedGenotyper (v.3.6) for variant calling (extremely relaxed settings, no filtration). I found a false-negative variant (chr7:117188684T>G) that is clearly visible in IGV. But if I run UnifiedGenotyper with the same settings but in EMIT_ALL_SITES mode, the variant is detected with high quality. Why the variant is not detected in EMIT_VARIANTS_ONLY mode?
Here is my commands:
java -jar GenomeAnalysisTK.jar -R /data/reference/hg19.fasta -T UnifiedGenotyper -I /data/sample_data.bam -stand_call_conf 1 -stand_emit_conf 1 -L /data/targets.bed --output_mode EMIT_VARIANTS_ONLY -o /data/emit_variants_only.vcf
java -jar GenomeAnalysisTK.jar -R /data/reference/hg19.fasta -T UnifiedGenotyper -I /data/sample_data.bam -stand_call_conf 1 -stand_emit_conf 1 -L /data/targets.bed --output_mode EMIT_ALL_SITES -o /data/emit_all_sites.vcf