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 it be better if I seperate the SNP and INDEL when I perform VQSR, like this:

• SNP.raw.vcf , INDEL.raw.vcf <- Seperate_SNP_INDEL(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 !