A few updates
A few updates

1. Now ignores rare invalid alignments due to bugs in earlier BWA
versions (e.g. alignments to Ns, no match to references), instead of
throwing out warnings.
2. Improvements in artifact detection in amplicon mode.
3. Added two options: -i and -M.  -i is for RNA-Seq and will output
splice junction read counts.  Useful if you're interested in
novel/alternative splicing and their relative expression.  -M (default
25) is the number of minimum matching bp in a read for it to be used for
variant calling.  Useful in amplicon where only matching sequences are
primers.
4. You can use "-k 0" to turn off local realignment or hyplotype calling
completely for Ion or PacBio where there're too many indels.

AstraZeneca-NGS/VarDict,chapmanb/VarDict,AstraZeneca-NGS/VarDict,AstraZeneca-NGS/VarDict,chapmanb/VarDict,chapmanb/VarDict