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different Filter output results between UnifiedGenotyper (Lite version) and UnifiedGenotyper (1.6.7)

java -Xmx6g -jar /pathto/GenomeAnalysisTKLite-2.2-16-g2cc9ef8/GenomeAnalysisTKLite.jar \
-T /pathto/UnifiedGenotyper \
-glm SNP \
-R /pathto/human_g1k_v37.fasta \
-I /pathto/NA10855.realign.recal.bam \
-L /pathto/target.intervals \
--dbsnp /pathto/dbsnp_135.b37.vcf \
-o GATKL/all.SNP.vcf

"Filter" column for most snp from VCF show only dot "." instead of "PASS". A few of those show "Low Qual"

CHROM POS ID REF ALT QUAL FILTER

1 9097241 rs5840 C T 1325.77 .
1 9097251 rs1063137 A G 1282.77 .

However, when I analyze the same Bam using the older version of GATK, filter column for most SNP from VCF show "PASS".

java -Xmx6g -jar /pathto/GenomeAnalysisTK-1.6-7-g2be5704/GenomeAnalysisTK.jar \
-T /pathto/UnifiedGenotyper \
-glm SNP \
-R /pathto/human_g1k_v37.fasta \
-I /pathto/NA10855.realign.recal.bam \
-L /pathto/target.intervals \
--dbsnp /pathto/dbsnp_135.b37.vcf \
-o GATKL/all.SNP.vcf

CHROM POS ID REF ALT QUAL FILTER

1 9097241 rs5840 C T 1324.32 PASS
1 9097251 rs1063137 A G 1281.28 PASS

Thank you.

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