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Indel normalization + left alignment for VQSR
Could you please inform me whether it is necessary to
normalize + left align INDELs before performing VQSR. Since all the training data sets are normalized and left aligned, how does it effect when the input VCF is not normalized and left aligned ?
Another question is, would you recommend performing VQSR for SNP and INDEL separately in two different VCF files (in one VCF files, there might be multi-allelic sites, which have both SNPs and INDELs.