Changes

; Map Reads with Appropriate Read Mapper

; Map Reads with Appropriate Read Mapper

: Currently, [bio-bwa.sourceforge.net/bwa.shtm BWA] is a convenient, widely used read mapper.

: Currently, [http://bio-bwa.sourceforge.net/bwa.shtm BWA] is a convenient, widely used read mapper.

; Mark Duplicate Reads

; Mark Duplicate Reads

; Recalibrate Base Quality Scores

; Recalibrate Base Quality Scores

: Base quality scores can be updated by comparing sites that are unlikely to vary (such as those not currently reported as variants in dbSNP or in the most recent [[1000 Genome Project]] analyses.

: Base quality scores can be updated by comparing sites that are unlikely to vary (such as those not currently reported as variants in dbSNP or in the most recent [http://www.1000genomes.org 1000 Genomes Project] analyses.

; Update Base Quality Score Metrics

; Update Base Quality Score Metrics

; Local Realignment Filter

; Local Realignment Filter

: Consider removing single nucleotide variants at sites where local realignment of all covering sequence reads suggests that a length polymorphism is present in the population.

: Consider removing single nucleotide variants at sites where local realignment of all covering sequence reads suggests that an [[indel]] polymorphism is present in the population.

; Read Depth

; Read Depth

: Consider filtering out variants at sites where total read depth is unusually low. Unfortunately, capture protocols introduce very large amounts of variation in sequencing depth and it is usually not possible to accurately filter out sites sequenced at very high depth.  

: Consider filtering out variants at sites where total read depth is unusually low. Unfortunately, capture protocols introduce very large amounts of variation in sequencing depth and it is usually not possible to accurately filter out sites sequenced at very high depth.

 

: Check whether each variant allele is supported by reads that map to both strands. Variants that are supported by reads on only one strand are almost always false positives.

= Special Considerations for Admixed Samples =

= Special Considerations for Admixed Samples =

== Burden Tests ==

== Burden Tests ==

The same analyses that were originally carried for single variants should be carried out for groups of rare variants. In principle, one could simple use the presence of a rare variant (or a particular class of rare variant, such as a non-synonymous variant or a newly discovered variant) as a predictor and repeat the logistic regression, linear regression or genotype regression described above. For an initial pass, I think the precise form of this analysis is not critical, because the next step is to...

The same analyses that were originally carried for single variants should be carried out for groups of rare variants. In principle, one could simply use the presence of a rare variant (or a particular class of rare variant, such as a non-synonymous variant or a newly discovered variant) as a predictor and repeat the logistic regression, linear regression or genotype regression described above. For an initial pass, I think the precise form of this analysis is not critical, because the next step is to...

== More Q-Q Plots ==

== More Q-Q Plots ==