---
name: "samtoh5"
section: "1"
platform: "linux"
package: "blasr"
version: "5.3+0-1"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/samtoh5"
---

# samtoh5(1)

convert a SAM file to cmp.h5 format

## NAME

samtoh5 - convert a SAM file to cmp.h5 format

## SYNOPSIS

**samtoh5** *in.sam* *reference.fasta* *out.cmp.h5* \[*options*\]

## OPTIONS

- *in.sam*

  Input SAM file.

- *reference.fasta*

  Reference used to generate reads.

- *out.cmp.h5*

  Output cmp.h5 file.

- **-smrtTitle**

  Use this option when converting alignments generated from reads produced by the [**pls2fasta**(1)](/pls2fasta/1.md) from bas.h5 files by parsing read coordinates from the SMRT read title. The title is in the format */name/hole/coordinates*, where coordinates are in the format \\d+\_\\d+, and represent the interval of the read that was aligned.

- **-readType** *value*

  Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA'

- **-verbosity** *value*

  Set desired verbosity.

- **-useShortRefName**

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

- **-copyQVs**

  Copy all QVs available in the SAM file into the cmp.h5 file. This includes things like InsertionQV and DeletionTag.

## NOTES

Because SAM has optional tags that have different meanings in different programs, careful usage is required in order to have proper output. The "xs" tag in bwa-sw is used to show the suboptimal score, but in PacBio SAM ([**blasr**(1)](/blasr/1.md)) it is defined as the start in the query sequence of the alignment. When **-smrtTitle** is specified, the xs tag is ignored, but when it is not specified, the coordinates given by the xs and xe tags are used to define the interval of a read that is aligned. The CIGAR string is relative to this interval.

## SEE ALSO

[**blasr**(1)](/blasr/1.md) [**loadPulses**(1)](/loadPulses/1.md) [**pls2fasta**(1)](/pls2fasta/1.md) [**samFilter**(1)](/samFilter/1.md) [**samtom4**(1)](/samtom4/1.md) [**sawriter**(1)](/sawriter/1.md) [**sdpMatcher**(1)](/sdpMatcher/1.md) [**toAfg**(1)](/toAfg/1.md)