Bioinformatics with Python Cookbook - Second Edition

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Although we will discuss data filtering in the Studying genome accessibility and filtering SNP data recipe in this chapter, it's not our objective to explain the SAM format in detail or give a detailed course in data filtering. This task will require a book of its own, but with the basics of pysam, you can navigate through SAM/BAM files. However, in the last recipe of this chapter, we will take a look at extracting genome-wide metrics from BAM files (via annotations on VCF files that represent metrics of BAM files) for the purpose of understanding the overall quality of our dataset.

You will probably have very large data files to work with. It's possible that some BAM processing will take too much time. One of the first approaches ...