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- Learn about SAM/BAM format and how to index the output from mapping for further analysis.
- Extract information about how reads were mapped from a SAM/BAM file.
Theory
SAM/BAM files act as repositories
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Although . Although most mappers assume FASTQ input files and output SAM files, the SAM file concept is intended to be a working repository/database of sequences that can be used at any stage of analysis. It is general enough to hold the alignments from multiple different samples within one BAM file so that, for example, a Bayesian genotyping tool can formulate a stronger association with a putative alternate allele when it scans across an entire family rather than separately through individuals. This information is encoded in the RG field in the SAM file header and on each raw read.
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cds mkdir samtools_exercise cd samtools_exercise cp /corral-repl/utexas/BioITeam$BI/web/yeast_stuff/yeast_chip.sam . |
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