Notebook bam

BAM files with sequence alignments sorted by genomic position seem to be the new currency of exchange for large-scale human genome sequencing projects. This is convenient and practical in many ways for many people. But in my current research I work a lot with tools that only want/need the sequence information and, for whatever reasons, support only FASTA or …

In which I explore read alignments in SAM format and discuss the pros and cons of various approaches to distinguishing perfect matches from imperfect matches.

tl;dr? It's fine, just ignore secondary/supplementary alignments and don't disable reporting of unaligned reads.