---
name: "gt-compreads-refcompress"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-compreads-refcompress"
---

# gt-compreads-refcompress(1)

Generates compact encoding for fastq data using Reference Compressed Reads (RCR).

## NAME

gt-compreads-refcompress - Generates compact encoding for fastq data using Reference Compressed Reads (RCR).

## SYNOPSIS

**gt compreads refcompress** \[option ...\] (-bam file -ref file)

## DESCRIPTION

- **-v** \[*yes\|no*\]

  be verbose (default: no)

- **-mquals** \[*yes\|no*\]

  store mapping quality for each read (default: no)

- **-quals** \[*yes\|no*\]

  store all quality values for each read, this implies enabling of option "vquals" (default: no)

- **-vquals** \[*yes\|no*\]

  store quality values of read positions having variations compared to reference (default: no)

- **-descs** \[*yes\|no*\]

  store read name for each read (default: no)

- **-ureads** \[*yes\|no*\]

  store unmapped reads in a separated fastq file (base name will be the value given in name and suffix will be " \_unmapped.fastq" (default: no)

- **-ref** \[*string*\]

  Index file (generated by the gt encseq tool) for reference genome. (default: undefined)

- **-bam** \[*string*\]

  File containing alignment of reads to genome (sorted ".bam" file). (default: undefined)

- **-name** \[*string*\]

  specify base name for RCR to be generated. If not set, base name will be set to base name of value given for option "bam" (default: undefined)

- **-help**

  display help and exit

- **-version**

  display version information and exit

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.