39 recalibrate quality scores the raw quality scores

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Unformatted text preview: M file. –  Does not align reads with indels! 34 35 SNP Calling SoIware Packages •  SOAPsnp is a member of the SOAP (Short Oligonucleo2de Analysis Package). –  The program is a resequencing u/lity that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference. –  The SNPs can then be iden/fied on the consensus sequence through the comparison with the reference. –  Developed at BGI. 36 37 Sequencing reads Align reads to reference genome Prior probability of each genotype Recalibrate quality scores Calculate the likelihood of each genotyoe Inferred genotype via Bayes’ theorem 38 Read Alignment •  Reads are aligned to the reference using some type of alignment program (GATK uses BWA, SOAPsnp uses SOAP). •...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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