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Will it be different if I seperate snp and indel to run VQSR
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 !