Getting ready

As discussed in the previous recipe, we will use data from the 1,000 Genomes Project. We will use the exome alignment for chromosome 20 of female NA18489. This is just 312 MB. The whole exome alignment for this individual is 14.2 GB, and the whole genome alignment (at a low coverage of 4x) is 40.1 GB. This data is a paired-end with reads of 76 bp. This is common nowadays, but slightly more complex to process. We will take this into account. If your data is not paired, just simplify the following recipe appropriately.

As usual, if you use Notebook, the cell at the top of Chapter02/Working_with_BAM.ipynb will download the data for you. If you don't use Notebooks, get the data from our dataset list at https://github.com/PacktPublishing/Bioinformatics-with-Python-Cookbook-Second-Edition/blob/master/Datasets.ipynb. The files you will want are NA18490_20_exome.bam and NA18490_20_exome.bam.bai.

We will use pysam, a Python wrapper to the SAMtools C API. This was installed in Chapter 1, Python and the Surrounding Software Ecology.