---
name: "samtom4"
section: "1"
platform: "linux"
package: "blasr"
version: "5.3+0-1"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/samtom4"
---

# samtom4(1)

Convert a SAM file generated by blasr(1) to M4 format

## NAME

samtom4 - Convert a SAM file generated by [**blasr**(1)](/blasr/1.md) to M4 format

## SYNOPSIS

**samtom4** *in.sam* *reference.fasta* *out.m4* \[*options*\]

## OPTIONS

- *in.sam*

  Input SAM file, which is produced by blasr.

- *reference.fasta*

  Reference used to generate *file.sam*.

- *out.m4*

  Output in [**blasr**(1)](/blasr/1.md) M4 format.

- **-header**

  Print M4 header.

- **-useShortRefName**

  Use abbreviated reference names obtained from *file.sam* instead of using full names from *reference.fasta*.

## SEE ALSO

[**blasr**(1)](/blasr/1.md) [**loadPulses**(1)](/loadPulses/1.md) [**pls2fasta**(1)](/pls2fasta/1.md) [**samFilter**(1)](/samFilter/1.md) [**samtoh5**(1)](/samtoh5/1.md) [**sawriter**(1)](/sawriter/1.md) [**sdpMatcher**(1)](/sdpMatcher/1.md) [**toAfg**(1)](/toAfg/1.md)