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Hi All, I have used GATK UnifiedGenotyper to generate a raw.vcf file. Now I want to use GATK VQSR to get a more accurate result ,and I follow this protocol:

snp.model <- BuildErrorModelWithVQSR(raw.vcf, SNP);
indel.model <- BuildErrorModelWithVQSR(raw.vcf, INDEL);
recalibratedSNPs.rawIndels.vcf <- ApplyRecalibration(raw.vcf, snp.model, SNP);
analysisReady.vcf <- ApplyRecalibration(recalibratedSNPs.rawIndels.vcf, indel.model, INDEL);

I wanna know will the it be better if I seperate the SNP and INDEL to run VQSR, like this:

SNP.raw.vcf , INDEL.raw.vcf <- SeperateSNPINDEL(raw.vcf);
snp.model <- BuildErrorModelWithVQSR(SNP.raw.vcf, SNP);
indel.model <- BuildErrorModelWithVQSR( INDEL.raw.vcf, INDEL);
SNP_analysisReady.vcf <- ApplyRecalibration(SNP.raw.vcf, snp.model, SNP);
INDEL_analysisReady.vcf <- ApplyRecalibration(INDEL.raw.vcf, INDEL.model, SNP);

Thanks a lot !

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