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==Insertion/Deletion ratios, Coding Regions and Overlap analysis==
==Insertion/Deletion ratios, Coding Regions and Overlap analysis==
You can obtain measure of insertion deletion ratios, coding region indels and sensitivity analysis by using the profile_indels analysis.
vt profile_indels -g indel.reference.txt -r ~/ref/vt/grch37/hs37d5.fa mills.normalized.sites.bcf
vt profile_indels -g indel.reference.txt -r ~/ref/vt/grch37/hs37d5.fa mills.normalized.sites.bcf
Precision 0.9%
Precision 0.9%
Sensitivity 0.2%
Sensitivity 0.2%
Ins/Del ratios: Reference alignment based methods tend to be biased towards the detection of deletions. This provides a useful measure for discovery Indel sets to show the varying degree of biasness.
Coding region analysis: Coding region Indels may be categorised as Frame shift Indels and Non frameshift Indels. A lower proportion of Frameshift Indels may indicate a better quality data set but this depends also on the individuals sequenced.
Overlap analysis: overlap analysis with other data sets is an indicator of sensitivity.
dbsnp: contains Indels submitted from everywhere, I am not sure what does this represent exactly.
Mills: contains doublehit common indels from the Mills. et al paper and is a relatively good measure of sensitivity for common variants. Because not all Indels in this set is expected to be present in your sample, this actually gives you an underestimate of sensitivity.
Mills chip: This is a subset of the Mills data set. There are genotypes here that are useful for subsetting polymophic subsets of variants that are present in samples common with your data set, this can potentially provide a better estimate of sensitivity. In general not very useful unless you happen to be working on 1000 Genomes data or any data set who's individuals are commonly studied.
Affy Exome Chip: This contains somewhat rare variants in exonic regions and is useful for exome chip analysis. You should subset your exome data to exome region Indels before comparing against this data set.
==STR ==
==STR ==
