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lecture-7 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 4, Lecture 7 István Albert Bioinformatics Consulting Center Penn State
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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
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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
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SAMtools A suite of programs to manipulate and process SAM files available actions with samtools
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Most actions will provide help on their usage
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Convert to BAM samtools view Sb input.sam > output.bam
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Sort/Index BAM file
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Filtering SAM/BAM files
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Flags are using a bitwise representation 1 = 00000001 paired end read
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