Compare multiple alignment results' aligned bases I have aligned a nanopore data set to a reference genome with graphmap, minimap2 and BLASR. The alignment results are stored in BAM files. 

I would like to do some concordance assessment, looking at the number of base pairs that are mapped to the same position by different aligner.   

Are there any tools or ways that allow me to do this effectively?
I don't know of a single tool that can read multiple sets of BAM files and compare them. But you can use the Sam_Reader python3 module to create a csv file that summarizes each position in the genome for each of your 3 results and then compare them manually.

It should be installable with:

pip3 install sam_reader


And then generate the CSV with 

from sam_reader import Sam_Reader
my_files = Sam_Reader('my_bam_file_or_folder/')
my_files.per_base_stats(write_file='new_file.csv')


*but FYI this module requires pysam, which does not work on windows