.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SUBINDEL "1" "February 2020" "subindel 2.0.0+dfsg-1~bpo10+1" "User Commands"
.SH NAME
subindel \- detect short and long indels
.SH USAGE
.PP
subindel \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
.PP
SubIndel: detect short and long indels
.SS "Usage:"
.IP
subindel \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