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Jump to navigationJump to searchUnderstanding vcf-summary output (view source)
Revision as of 23:29, 16 June 2014
, 23:29, 16 June 2014→What should we expect from good SNP call sets?
* Because of natural selection, in exomes, we expect higher Ts/Tv in known SNPs than novel SNPs. This is because novel SNPs are more likely to be non-synonymous SNPs than synonymous SNPs. Please refer to [[SNP_Call_Set_Properties]] for additional information.
* Because of natural selection, in exomes, we expect higher Ts/Tv in known SNPs than novel SNPs. This is because novel SNPs are more likely to be non-synonymous SNPs than synonymous SNPs. Please refer to [[SNP_Call_Set_Properties]] for additional information.
* '''%dbSNP''' should be usually higher for '''PASS''' categories than others, indicating that known SNPs are more likely to pass filters. However, because dbSNP also contain false positive variants, we don't necessarily expect that '''%dbSNP''' go to zero even if the filtering works perfectly.
* '''%dbSNP''' should be usually higher for '''PASS''' categories than others, indicating that known SNPs are more likely to pass filters. However, because dbSNP also contain false positive variants, we don't necessarily expect that '''%dbSNP''' go to zero even if the filtering works perfectly.
* Because HM3 consist of common SNPs, this number should be high when the sample size is large. Typically, if the sample contains only Europeans, the expected values of '''%HM3 sens''' are around 90%. If the sample contains African ancestry, the number will be close to 95% of higher.
* Note that some callers uses the expected difference between Ts and Tv in their calling model as prior. In that case, Ts/Tv could be biased by the prior, and Ts/Tv may not be a good indicator of SNP qualities.
* Note that some callers uses the expected difference between Ts and Tv in their calling model as prior. In that case, Ts/Tv could be biased by the prior, and Ts/Tv may not be a good indicator of SNP qualities.
