How to use VariantRecalibrator ?

[zznx]

Hi, it took me a long time. If I could get some help, I would be extremely grateful.
What should I do to improve the outcome?

cohort.snps.tranches.pdf

CollectHsMetrics.txt

gatk VariantRecalibrator \
   -R /mnt/BioData/zhangjianxi/DataBases/WES/ref/Homo_sapiens_assembly38.fasta \
   -V gathered_cohort.vcf.gz \
   --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /mnt/BioData/zhangjianxi/DataBases/WES/hapmap_3.3.hg38.vcf.gz \
   --resource:omni,known=false,training=true,truth=false,prior=12.0 /mnt/BioData/zhangjianxi/DataBases/WES/1000G_omni2.5.hg38.vcf.gz \
   --resource:1000G,known=false,training=true,truth=false,prior=10.0 /mnt/BioData/zhangjianxi/DataBases/WES/hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gz \
   --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /mnt/BioData/zhangjianxi/DataBases/WES/Homo_sapiens_assembly38.dbsnp138.vcf.gz \
   -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
   -mode SNP \
   -O cohort.snps.recal \
   --tranches-file cohort.snps.tranches \
   --rscript-file cohort.snps.plots.R \
   -L /mnt/BioData/zhangjianxi/DataBases/WES/list.interval_list 2> VariantRecalibrator.log &

Best,
jianxi zhang

[zznx]

## htsjdk.samtools.metrics.StringHeader
# CollectVariantCallingMetrics --INPUT gathered_cohort.vcf.gz --OUTPUT cohort.raw.metrics --DBSNP /mnt/BioData/zhangjianxi/DataBases/WES/Homo_sapiens_assembly38.dbsnp138.vcf.gz --REFERENCE_SEQUENCE /mnt/BioData/zhangjianxi/DataBases/WES/ref/Homo_sapiens_assembly38.fasta --GVCF_INPUT false --THREAD_COUNT 1 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Sep 08 08:32:49 GMT 2025

## METRICS CLASS	picard.vcf.CollectVariantCallingMetrics$VariantCallingSummaryMetrics
TOTAL_SNPS	NUM_IN_DB_SNP	NOVEL_SNPS	FILTERED_SNPS	PCT_DBSNP	DBSNP_TITV	NOVEL_TITV	TOTAL_INDELS	NOVEL_INDELS	FILTERED_INDELS	PCT_DBSNP_INDELS	NUM_IN_DB_SNP_INDELS	DBSNP_INS_DEL_RATIO	NOVEL_INS_DEL_RATIO	TOTAL_MULTIALLELIC_SNPS	NUM_IN_DB_SNP_MULTIALLELIC	TOTAL_COMPLEX_INDELS	NUM_IN_DB_SNP_COMPLEX_INDELS	SNP_REFERENCE_BIAS	NUM_SINGLETONS
79919	65204	14715	0	0.815876	3.040151	2.15976	2601	1282	0	0.507113	1319	0.76573	0.56151	389	281	577	432	0.54436	22653

[zznx]

I should have known that NOVEL_TITV usually doesn't exceed 2.8?