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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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Code Block
languagebash
titleget a copy the yeast_pairedend.bam file from Nathan's scratch areayesterday to a new directory "samtools"
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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