GATKv2 UnifiedGenotyper SNP heterozygosity are extremely high!!!
When I use GATK UnifiedGenotyper to call SNP, I found that in the vcf files, ABHom SNPs are much higher(bigger than 5 times) than ABHet SNPs which is so abnormal. The following are the parameters I set.
GATK_UnifiedGenotype::java -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -l INFO -R ucsc.hg19.fasta -T UnifiedGenotyper -glm BOTH -nt 8 -A AlleleBalance -A DepthOfCoverage -A HaplotypeScore -stand_call_conf 50 -stand_emit_conf 10 --dbsnp dbsnp_135.hg19.vcf -dcov 50 -L **
GATK_VariantRecalibrator_SNP::java -Xmx4g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T VariantRecalibrator -R ucsc.hg19.fasta -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf -resource
mni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_135.hg19.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -mode SNP
GATK_VariantRecalibrator_INDEL::java -Xmx4g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T VariantRecalibrator -R ucsc.hg19.fasta -resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -an QD -an FS -an HaplotypeScore -an ReadPosRankSum -mode INDEL --maxGaussians 4
GATK_ApplyRecalibration::java -Xmx3g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T ApplyRecalibration -R ucsc.hg19.fasta --ts_filter_level 99.0
Does anyone encounter the same question as me? Thank you very much!
GATK_UnifiedGenotype::java -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -l INFO -R ucsc.hg19.fasta -T UnifiedGenotyper -glm BOTH -nt 8 -A AlleleBalance -A DepthOfCoverage -A HaplotypeScore -stand_call_conf 50 -stand_emit_conf 10 --dbsnp dbsnp_135.hg19.vcf -dcov 50 -L **
GATK_VariantRecalibrator_SNP::java -Xmx4g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T VariantRecalibrator -R ucsc.hg19.fasta -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf -resource
mni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_135.hg19.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -mode SNPGATK_VariantRecalibrator_INDEL::java -Xmx4g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T VariantRecalibrator -R ucsc.hg19.fasta -resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -an QD -an FS -an HaplotypeScore -an ReadPosRankSum -mode INDEL --maxGaussians 4
GATK_ApplyRecalibration::java -Xmx3g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T ApplyRecalibration -R ucsc.hg19.fasta --ts_filter_level 99.0
Does anyone encounter the same question as me? Thank you very much!