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) Report bugs to js18@sanger.ac.uk