Miseq应用初步经验（MiSeq Implementation in CGS）

MiSeq Implementation in CGS experience sharing,Tong Ming For 16 August 2014,Outlines,Data Producing Selection of targeted panel Preparation of libraries Sequencing inside the MiSeq Data Processing (WL Lab) Computing analysis Data Analysis bioinformatics Future endeavor,Outlines,Data Producing Selection of targeted panel Preparation of libraries Sequencing inside the MiSeq Data Processing (WL / HKU) Computing analysis Data Analysis bioinformatics Future endeavor,.bam,.fastq,.vcf,.els,.bam,.fastq,.vcf,.els,Summary for reads distribution,One SNP reported by Miseq result (FBN1:NM_000138:exon66:c.C8234G:p.S2745C),All reads mapped in the position, including duplicated reads and reads with bad MQ,.bam,.fastq,.vcf,.exl,If we removed those duplication and reads with low MQ, the result should be ref/ref,only 4 reads with G covered in the site, it is more likely to be a hom instead of het.,Miseq automatic pipeline did not remove duplication and used bad MQ reads for genotyping. By contrast, if we remove duplicates and used reads with MQ50), only 8 for G left, but 4 of them are duplications in this example. C, T was moved due to low MQ.,Not sufficient coverage!,Outlines,Data Producing Selection of targeted panel Preparation of libraries Sequencing inside the MiSeq Data Processing (HKU) Computing analysis Data Analysis bioinformatics Future endeavor,Benign by ClinVar,Pathogenic by ClinVar,c.6380-12_c.6380-13insT,Data Producing Selection of targeted panel Preparation of libraries Sequencing inside the MiSeq Data Processing (WL Lab) Computing analysis Data Analysis bioinformatics,Based on fastq file, total produced 1.2 Gb data from 12 samples !,Data Producing Selection of targeted panel Preparation of libraries Sequencing inside the MiSeq Data Processing (CGS ?) Computing analysis Data Analysis bioinformatics,Future Endeavor,Short term Targeted panel Marfan, NF, DMD RP Hypothyroid,Mid term Exome sequencing ARSCA Long term Accreditation Bioinformatic team,