1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Insertion/Deletion ratios, Coding Regions and Overlap analysis
Overlap analysis: overlap analysis with other data sets is an indicator of sensitivity.
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.
* dbsnp: contains Indels submitted from everywhere, I am not sure what does this represent exactly. But assuming most are real, then precision is a useful estimated quantity from this reference data set.
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: 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.
* 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.
* 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 ==
