Massive parallel sequencing produces a large number of small sequencing reads that have to be mapped to the reference human genome. BAM files are large binary files that contain the aligned sequenced reads. The BAM file will probably be the ideal intersection between genome center and exome data end user. Let’s start with samtools.īAM, here’s your exome. the program that translates chromosomal coordinates into positions within genes including the impact of a given mutation. Samtools is a bioinformatic workhorse to cut, format and extract data from large BAM files, DeNovoGear is the main program for the detection of de novo mutations, and annovar is the standard annotation tool, i.e. This is the first post describing my experience with the three essential tools for exome analysis in patient-parent trios: samtools, DeNovoGear and annovar. During the holidays, I tried to explore the possibility to analyze exomes on my laptop. Secondly, as exome sequencing has become a standard procedure, the analysis and interpretation of exome data will shift from genome centers to individual scientists as has happened before with the analysis of copy number variations. First, exome sequencing will slowly replaced by genome sequencing in cutting edge genomic science. Looking at 2013 unfolding, there will probably two trends. However, this is not a post about children’s books it’s about a likely 2013 trend in genomic research, the redefinition of the boundary between genome center and end user and the laptopification of life sciences. Given that we are currently reading through the original books almost on a daily basis due to the presence of a toddler in our home, mentioning *.sam files, *.bam files or sam2bam routines always makes me smile. The entire field of high-throughput genomics appears to be inspired by the American children’s book author Dr.
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