.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH SUBINDEL "1" "June 2017" "subindel 1.5.1+dfsg-4~bpo8+1" "User Commands"
.SH NAME
subindel \- detect short and long indels
.SH USAGE

\fBsubindel\fR \fB\-i\fR <SAM file> \fB\-g\fR <subread index> \fB\-o\fR <output VCF> {\-d <expected fragment distance>} {\-I <max indel length>} {\-\-paired\-end}
.SS "Example:"
.IP
subindel \fB\-i\fR my_paired_end_reads.SAM \fB\-g\fR my_index \fB\-o\fR my_result \fB\-d\fR 300 \fB\-I\fR 200 \fB\-\-paired\-end\fR