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Genome sequence analysis12/21/2023 ![]() To rebuild the sequence index, issue the following commands (they will take approximately 2 minutes to complete): The sequence index is typically not compatible across different BWA versions. This index lists the location of particular short words along the genome and can be used to seed and then extend particular matches. To quickly place short reads along the genome, BWA and other read mappers typically build a word index for the genome. The example dataset will be available in the workshop folder, so let's move thereīuilding an Index for Short Read Alignment Finally, we will use the LD refinement to increase the accuracy of our genotypes. We will compare the results of the variant calling on the low pass dataset with results from the exome sequencing of the same individual. We will then perform the variant calling by combining the results with mapped reads from the other 7 individuals to generate a list of polymorphic sites and estimate genotypes at each of these sites. We will first map reads for 3 individuals. To conserve time and disk-space, our analysis will focus on a small region of chromosome 20, from 33,500,000 to 33,600,000 bp. As with other 1000 Genomes Project samples, these individuals have been sequenced to an average depth of about 4x. Our dataset consists of 10 individuals sequenced by the 1000 Genomes Project. The dataset for the tutorial can be downloaded here Example Dataset If you are participating in the Sardinia Summer School, everything is already installed and you can move on. We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file). As part of the process, you will learn about many of the file formats commonly used to store next generation sequence data.įor questions or comments please contact Carlo Sidore. In this workshop, we will illustrate some of the essential steps in the analysis of next generation sequence data. 1.7 Genotype Refinement Using Linkage Disequilibrium Information.1.3 Building an Index for Short Read Alignment.
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