---
name: "samclip"
section: "1"
platform: "linux"
package: "samclip"
version: "0.4.0-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samclip"
---

# samclip(1)

filter SAM file for soft and hard clipped alignments

## NAME

samclip - filter SAM file for soft and hard clipped alignments

## SYNOPSIS

**samclip** *--ref ref.fa \< in.sam \> out.sam*

## USAGE

In connection with minimap2

-

  minimap2 ref.fa R1.fq R2.fq \| samclip --ref ref.fa \| samtools sort \> out.bam

## DESCRIPTION

Filter SAM file for soft & hard clipped alignments

## OPTIONS

- **--help**

  This help

- **--version**

  Print version and exit

- **--ref** FASTA

  Reference genome - needs FASTA.fai index

- **--max** NUM

  Maximum clip length to allow (default=5)

- **--invert**

  Output rejected SAM lines and ignore good ones

- **--debug**

  Print verbose debug info to stderr

- **--progress** N

  Print progress every NUM records (default=100000,none=0)

## SEE ALSO

-

  https://github.com/tseemann/samclip

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.