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Revision as of 23:55, 20 April 2010
, 23:55, 20 April 2010→Special Considerations for Admixed Samples
:* The number of unique and shared variants
:* The number of unique and shared variants
:* The number of transitions and transversions
:* The number of transitions and transversions
== Evaluate Variant Calls for Reference Samples ==
; If Previously Sequenced Samples Available, Assess Variant Calls There
: Assess concordance rate at non-reference sites
; If Duplicate Samples are Available, Assess Concordance
: Assess concordance rate at non-reference sites.
; If Nuclear Families are Available, Assess Mendelian Consistency
: When reporting rates of Mendelian inconsistencies, report these not on a per site basis but, instead, based on the number of sites with at least one non-reference call in the trio.
== Special Considerations for Admixed Samples ==
== Special Considerations for Admixed Samples ==
; Estimate Local Ancestry Using GWAS Data
; Estimate Local Ancestry Using GWAS Data
: For studies that include admixed samples, we should estimate local ancestry using GWAS data. If GWAS are not available, it is strongly recommended that these data should be generated. In principle, local ancestry estimates can be generated even before exome sequencing is complete.
: For studies that include admixed samples, we should estimate local ancestry using GWAS data. If GWAS are not available, it is strongly recommended that these data should be generated. In principle, local ancestry estimates can be generated even before exome sequencing is complete.
= Think You Are Done? =
'''No way!!!''' You still need a plan to call and evaluate short insertions and deletions as well as larger structural variants.
== Initial Association Analyses ==
== Initial Association Analyses ==
We anticipate that, at least early on, the initial association analysis of whole genome datasets in the context of complex trait association studies will focus on identifying and resolving quality control issues that might result in unexpected artifacts.
We anticipate that, at least early on, the initial association analysis of whole genome datasets in the context of complex trait association studies will focus on identifying and resolving quality control issues that might result in unexpected artifacts.
