I'm trying to teach myself SAMtools/bedtools commands (on UNIX running on a VM). For practice, I have found a .bam file. I'm trying to find an online source which will show me how to do the following.
How many alignments does the set contain?
How many alignments show the read’s mate unmapped?
How many alignments contain a deletion (D)?
How many alignments show the read’s mate mapped to the same chromosome?
How many alignments are spliced?
Extract only the alignments in the range “Chr?:10,677,300-11,894,100”, corresponding to a locus of interest.
Any help would be greatly appreciated! or even a nod in the right direction. Thanks for reading!