Changes

* 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 ==

==to document==

Annotation of STRs is really important.  Show example of a deceptive single base pair variant

* Annotation of STRs is really important.  Show example of a deceptive single base pair variant

 

* Can check concordance of genotypes between callers - partitiion

 

* Type of Indels - homopolymer types and STR types and isolated, Adjacent SNPs ,Adjacent MNPs,Clumping variants

 

* genotype likelihood concordance

* concordance stratified by indel length or tract length

 

* mendelian concordance by tract length

 

 

 

 

 

 

 

 

Can check concordance of genotypes between callers

 

 

 

 

AF - rare versus common

Type of Indels - homopolymer types and STR types and isolated

Adjacent SNPs

Adjacent MNPs

Clumping variants

 

 

genotype likelihood concordance

concordance stratified by indel length or tract length

mendelian concordance by tract length