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Revision as of 07:14, 21 April 2010
, 07:14, 21 April 2010→Read Mapping
; 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, [bio-bwa.sourceforge.net/bwa.shtm BWA] is a convenient, widely used read mapper.
; Mark Duplicate Reads
: Duplicate reads, whether generated as PCR artifacts during library preparation or optical duplicates during image analysis and base-calling, can mislead variant calling algorithms. To avoid problems, one typically removes from consideration all reads that appear to map at exactly the same location (for paired ends, only reads for which both ends map to the same locations are excluded.)
; Basic Mapping Statistics
; Basic Mapping Statistics
