Setup output directory.
If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.
Index the reference 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 value 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?
Is not practical, since we will lose vital VCF formatting and may not be able to use this file in the futre.
Will preserve all lines that don't have an AF1=0 value.
Is a better way of doing it inline and not requiring you to make another file.
Determining Differences Between Aligners.
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.