Lecture-7-handouts - Binary SAM files Practical Bioinformatics for Life Scientists SAM file Week 4 Lecture 7 Istvn Albert Bioinformatics Consulting

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9/13/2011 1 Practical Bioinformatics for Life Scientists Week 4, Lecture 7 István Albert Bioinformatics Consulting Center Penn State Binary SAM files SAM file: information on the alignment of each read optimized for readability and sequential access BAM (binary SAM): compression saves space (optimized for size) may be sorted + indexed location query (optimized for random access) the file is not readable by eye anymore SAM/BAM hierarchy SAM file Sorted SAM file BAM file Sorted BAM file Indexed BAM file Some tools have certain requirements of what type of SAM/BAM they take SAMtools A suite of programs to manipulate and process SAM files available actions with samtools
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9/13/2011 2 Most actions will provide help on their usage Convert to BAM samtools view Sb input.sam > output.bam Sort/Index BAM file Filtering SAM/BAM files
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9/13/2011 3 Flags are using a bitwise representation 1 = 00000001 paired end read
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This note was uploaded on 02/29/2012 for the course BMMB 597D taught by Professor Istvanalbert during the Fall '11 term at Pennsylvania State University, University Park.

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Lecture-7-handouts - Binary SAM files Practical Bioinformatics for Life Scientists SAM file Week 4 Lecture 7 Istvn Albert Bioinformatics Consulting

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