2.3 - Mapping
The goal of mapping is to align the reads of each fastq library to the respective regions of the reference genome where the reads likely originated. Mapping the reads to the reference genome typically involves the alignment of millions of short reads to the genome using algorithms for fast alignment implemented using mapper tools.
To complete mapping with the SNP/Indel protocol, we map the preprocessed fastq files on the hg19 reference. The Step-by-Step menu offers you two DNAseq mappers: Bowtie2 (Langmead and Salzberg 2012) and BWA (Li and Durbin 2009). In this tutorial we will use BWA because is the typical mapper for exome analysis. To this end, please go to the Step-by-Step menu path, SNP/Indels → Mapping → DNAseq mappers → BWA and proceed as indicated in Video 4
Video 4. Mapping fastq libraries on the hg19 genome with the BWA implementation of VariantSeq.
Expected results from mapping analysis
When BWA is complete, you will receive a bam file per sample with the reads mapped against the reference genome.
The expected results of this step are available in the following link Mapping
Remember you can check how the job was completed by accessing the job tracking panel. Pay particular focus on the log file metrics showing the % or reads successfully mapped. An acceptable value is more than 80% of reads mapped per fastq library. If the % is lower than 70% try to preprocess the samples again for better cleaning of the fastq libraries.
To learn more about BWA see, http://bio-bwa.sourceforge.net