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

# iHS(1)

## NAME

**iHS**

## SYNOPSIS

**iHS** –target 0,1,2,3,4,5,6,7 –file my.phased.vcf  –region chr1:1-1000 \> STDOUT 2\> STDERR

## DESCRIPTION

**iHS** calculates the integrated haplotype score which measures the relative decay of extended haplotype homozygosity (EHH) for the reference and alternative alleles at a site (see: voight et al. 2006, Spiech & Hernandez 2014).

## OPTIONS

-

  ```
  Our code is highly concordant with both implementations mentioned. However, we do not set an upper limit to the allele frequency.  **iHS** can be run without a genetic map, in which case the change in EHH is integrated over a constant.  Human genetic maps for GRCh36 and GRCh37 (hg18 & hg19) can be found at: http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/ . **iHS** by default interpolates SNV positions to genetic position (you don't need a genetic position for every VCF entry in the map file).
  **iHS** analyses requires normalization by allele frequency.  It is important that **iHS** is calculated over large regions so that the normalization does not down weight real signals.  For genome-wide runs it is recommended to run slightly overlapping windows and throwing out values that fail integration (columns 7 & 8 in the output) and then removing duplicates by using the 'sort' and 'uniq' linux commands.  Normalization of the output is as simple as running 'normalize-**iHS**'.
       **iHS** calculates the integrated ratio of haplotype decay between the reference and non-reference allele.
  Output : 4 columns :
       1. seqid
       2. position
       3. target allele frequency
       4. integrated EHH (alternative)
       5. integrated EHH (reference)
       6. **iHS** ln(iEHHalt/iEHHref)
       7. != 0 integration failure
       8. != 0 integration failure
  Params:
         required: t,target  <STRING>  A zero base comma separated list of target
                                       individuals corresponding to VCF columns
         required: r,region  <STRING>  A tabix compliant genomic range
                                       format: "seqid:start-end" or "seqid"
         required: f,file    <STRING>  Proper formatted and phased VCF.
         required: y,type    <STRING>  Genotype likelihood format: GT,PL,GL,GP
         optional: a,af      <DOUBLE>  Alternative alleles with frquences less
                                       than [0.05] are skipped.
         optional: x,threads <INT>     Number of CPUS [1].
         recommended: g,gen <STRING>   A PLINK formatted map file.
  Type: statistics
  ```

## 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.