.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH SAMCLIP "1" "May 2020" "samclip 0.4.0" "User Commands"
.SH NAME
samclip \- filter SAM file for soft and hard clipped alignments
.SH SYNOPSIS
.B samclip
\fI--ref ref.fa < in.sam > out.sam\fR
.SH USAGE
In connection with minimap2
.IP
minimap2 ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam
.SH DESCRIPTION
Filter SAM file for soft & hard clipped alignments
.SH OPTIONS
.TP
\fB\-\-help\fR
This help
.TP
\fB\-\-version\fR
Print version and exit
.TP
\fB\-\-ref\fR FASTA
Reference genome \- needs FASTA.fai index
.TP
\fB\-\-max\fR NUM
Maximum clip length to allow (default=5)
.TP
\fB\-\-invert\fR
Output rejected SAM lines and ignore good ones
.TP
\fB\-\-debug\fR
Print verbose debug info to stderr
.TP
\fB\-\-progress\fR N
Print progress every NUM records (default=100000,none=0)
.SH SEE ALSO
.IP
https://github.com/tseemann/samclip
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.