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Introduction to Samtools - manipulating and filtering bam files
As Nathan we showed you yesterday, the main type of output from aligning reads to a databases is a binary alignment file, or BAM file. These files are compressed, so they can't be viewed using standard unix file viewers such as more, less and head. Samtools allows you to manipulate the .bam files - they can be converted into a non-binary format (SAM format specification here) and can also be ordered and sorted based on the quality of the alignment. This is a good way to remove low quality reads, or make a BAM file restricted to a single chromosome.
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ssh user@login8.stampede.tacc.utexas.edu cdscd $SCRATCH/core_ngs mkdir samtools cd samtools cp /scratch/02423/nsabell/$SCRATCH/core_ngs/alignment/bam/yeast_pairedend.bam . |
Sorting and Indexing a bam file: samtools index, sort
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