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Revision as of 00:27, 21 April 2010
, 00:27, 21 April 2010→Special Considerations for Admixed Samples
: 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.
: 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 ==
== Variant Filters ==
Initial sets of SNP calls invariable will include many false positives. As a proportion of total variants called, the number of false positives is likely to increase as more and more samples are sequenced. To keep the number of false positives under control, it is important to both apply an increasingly strict set of quality control filters but also to experimentally validate some newly discovered variants. Many of these filters are currently implemented in [[GATK]].
; Mapping Quality Filter
: Consider removing variants at sides with low mapping quality scores. Even if the average mapping quality score for a site is high, consider removing variants at sites where a large fraction of reads have low mapping quality scores.
; Allele Balance Filter
: Among individuals who are assigned an heterozygous genotype, check the proportion of reads supporting each allele. Consider filtering out variants where one of the alleles accounts for <30% of reads.
; 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 also accurately filter out sites sequenced at very high depth.
= Special Considerations for Admixed Samples =
; Estimate Local Ancestry Using GWAS Data
; Estimate Local Ancestry Using GWAS Data
