---
name: "hapLrt"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/hapLrt"
---

# hapLrt(1)

## NAME

**hapLrt**

## SYNOPSIS

hapLRT –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –type GP –file my.vcf

## DESCRIPTION

HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribution. The sign denotes if the target has longer haplotypes (1) or the background (-1).

## OPTIONS

-

  ```
  Output : 4 columns :
       1. seqid
       2. position
       3. mean target haplotype length
       4. mean background haplotype length
       5. p-value from LRT
       6. sign
  required: t,target     -- argument: a zero base comma separated list of target individuals corresponding to VCF columns
  required: b,background -- argument: a zero base comma separated list of background individuals corresponding to VCF columns
  required: f,file       -- argument: a properly formatted phased VCF file
  required: y,type       -- argument: type of genotype likelihood: PL, GL, GT or GP
  optional: r,region     -- argument: a genomic range to calculate **hapLrt** on in the format : "seqid:start-end" or "seqid"
  Type: genotype
  ```

## EXIT VALUES

- **0**

  Success

- **not 0**

  Failure

## SEE ALSO

[**vcflib**(1)](/vcflib/1.md)

## OTHER

## LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

## AUTHORS

Erik Garrison and vcflib contributors.