Analyses of Indels
Motivation
This wiki page will details the useful steps in analysing Indels. In particular it is to help the group in understanding the issues and perform the analyses quickly without reinventing the wheel.
Tools
You can download vt and have some working knowledge of PERL to do stuff that vt does not support.
Coding regions
The proportion of frameshift Indels amongst coding region indels is a potential indicator of quality.
STR
Annotation of STRs is really important. Show example of a deceptive single base pair variant
Normalization
Indel representation is not unique, you should normalize them and remove duplicates.
Annotation of Indels
Examining Mendelian Errors
Useful to have call sets from several different callers
Concordance
Can check concordance of genotypes between callers
Overlapping percentages with known data sets
With Mills with dbSNP with exome chips with genotyping chips if available
Useful stratifying features
AF - rare versus common Indel length - computed naively versus tract length Allele frequency bins Type of Indels - homopolymer types and STR types and isolated Adjacent SNPs Adjacent MNPs Clumping variants
Other useful evaluations
genotype likelihood concordance concordance stratified by indel length or tract length mendelian concordance by tract length
