```
docker run --rm quay.io/biocontainers/bwa:0.7.19--h577a1d6_1 bwa sampe
```

Usage:   bwa sampe [options] <prefix> <in1.sai> <in2.sai> <in1.fq> <in2.fq>

Options: -a INT   maximum insert size [500]
         -o INT   maximum occurrences for one end [100000]
         -n INT   maximum hits to output for paired reads [3]
         -N INT   maximum hits to output for discordant pairs [10]
         -c FLOAT prior of chimeric rate (lower bound) [1.0e-05]
         -f FILE  sam file to output results to [stdout]
         -r STR   read group header line such as `@RG\tID:foo\tSM:bar' [null]
         -P       preload index into memory (for base-space reads only)
         -s       disable Smith-Waterman for the unmapped mate
         -A       disable insert size estimate (force -s)

Notes: 1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.
       2. For reads shorter than 30bp, applying a smaller -o is recommended to
          to get a sensible speed at the cost of pairing accuracy.

