UnifiedGenotyper different results depending on the output mode

tomkinatomkina RussiaMember
edited September 2016 in Ask the GATK team

Hello

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

Thanks,
Tamara

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