Usage: sga var2vcf [OPTION] ... BAMFILE
Convert the sequence aligned to a reference in BAMFILE into a VCF file of differences

      --help                           display this help and exit
      -v, --verbose                    display verbose output
      -r, --reference=FILE             read the reference sequences from FILE
      -o, --outfile=FILE               write the results to FILE
      -q, --min-quality=Q              discard variants with mapping quality less than Q (default: 1)

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