what does this mean in VQSR output vcf files?
Posted in Ask the GATK team | Last updated on 2013-11-01 20:04:57


Comments (1)

I have the following entries in my vcf files output from VQSR. What does the "VQSRTrancheINDEL99.00to99.90" string mean? did they fail the recalibration?

PASS
VQSRTrancheINDEL99.00to99.90
VQSRTrancheINDEL99.00to99.90
VQSRTrancheINDEL99.00to99.90
PASS
VQSRTrancheINDEL99.00to99.90
PASS
PASS
VQSRTrancheINDEL99.90to100.00
VQSRTrancheINDEL99.90to100.00
VQSRTrancheINDEL99.90to100.00
PASS
VQSRTrancheINDEL99.00to99.90
VQSRTrancheINDEL99.00to99.90

Below is the command I used:

java -Xmx6g -jar $CLASSPATH/GenomeAnalysisTK.jar \
-T ApplyRecalibration \
-R GATK_ref/hg19.fasta \
-nt 5 \
--input ../GATK/VQSR/parallel_batch/combined_raw.snps_indels.vcf \
-mode INDEL \
--ts_filter_level 99.0 \
-recalFile ../GATK/VQSR/parallel_batch/Indels/exome.indels.vcf.recal \
-tranchesFile ../GATK/VQSR/parallel_batch/Indels/exome.indels.tranches \
-o ../GATK/VQSR/parallel_batch/Indels/exome.indels.filtered.vcf

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