SAMtools is a quite of commands for dealing with databases of mapped reads. You'll be using it quite a bit throughout the course.
Right now, we'll be using it to call variants (find mutations) in the re-sequenced E. coli genome from the Introduction to mapping (bowtie, BWA). You will need the output SAM files from that tutorial to continue here.
Create a new output directory:
Lets copy over the read alignment file in the SAM format and the reference genome in FASTA format to the new directory, so that we don't have so many files cluttering our space up.
Index the reference file. (This isn't indexing it for mapping. It's indexing it so that SAMtools can quickly jump to a certain base.)
Take a look at the new file that was created by this command.
SAM is a text file, so it is slow to access information about a read. SAMtools and many of the commands that we will run later work on BAM files (essentially binary forms of the text SAM files). These can be loaded much more quickly. Typically, they also need to be sorted, so that when the program wants to look at all reads overlapping position 4,129,888 it can easily find them all at once without having to search through the entire BAM file.
Convert from SAM to BAM format.
Sort the BAM file.
Output VCF file.
VCF format has Allele Frequency tags denoted by AF1. Try the following command to see what values we have in our files.
For the data we are dealing with, predictions with an allele frequency not equal to 1 are not really applicable. How can we remove these lines from the file and continue on?
What does the -v flag do in grep?
Determining Differences Between Mappers.
Setup output directory and then change into it.
Bedtools is a suite of utility programs that work on a variety of file formats, one of which is conveniently VCF format. Using intersectBed and subtractBed we can find equal and different predictions between mappers.
Finding alike mutations.
Finding unique mutations for each mapper.