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VCF Normalisation is required ?

Hello

I had few questions 1) Is normalisation step is necessary for a VCF file ? 2) How to check true positives, false positives, false negatives, false positives ? (Is their any tools does Positive prediction score )

Thanks for your comments.

genome next-gen snp
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updated by Carlos Borroto Carlos Borroto • written by pinn pinn

Hello pinninti1991reddy!

Please follow up on your questions. See C: Readgroups for a bam file ?

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Ram Ram

1 answer

1) Yes, you do need to do normalization of the VCF, however the tools below will help you with that.

2) The main tools I know of are Illumina's hap.py and Real Time Genomics' vcfeval. Both are tools recommended by the PrecicionFDA Truth Challenge.

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written by Carlos Borroto Carlos Borroto

Thanks, Is vcf normalization should be performed for a raw vcf or for an annotated vcf ? I'm little confused. It should be for a raw vcf isn't ? From a vcf how to count TP, FP & FN variants is their any tool ?

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written by pinn pinn

Both hap.py and vcfeval perform comparison at the level of underlying haplotypes asserted by the entries in the VCF, so they don't require up-front normalization. Normalization is mostly useful if you are trying to do comparisons using tools that don't operate at the haplotype level (but such tools are much less sophisticated, and can't for example determine when you have multiple SNPs that together are equivalent to a MNP).

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written by Len Trigg Len Trigg

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