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May 22, 2014 · Commonly, SAM files are processed in this order: SAM files are converted into BAM files ( samstools view) BAM files are sorted by reference coordinates ( samtools sort) Sorted BAM files are indexed ( samtools index) Each step above can be done with commands below. samtools view -bS <samfile> > <bamfile> samtools sort <bamfile> <prefix of sorted .... May 17, 2017 · BAM files are sorted by reference coordinates (samtools sort) Sorted BAM files are indexed (samtools index) Sorted, indexed BAM files are filtered based on location, flags, mapping quality (samtools view with filtering options) Take a look here for a detailed manual page for each function in samtools..

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