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% IHS(1) iHS (vcflib) | iHS (VCF statistics)
% Erik Garrison and vcflib contributors
# 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](./vcflib.md)(1)
# OTHER
## Source code
[iHS.cpp](https://github.com/vcflib/vcflib/blob/master/src/iHS.cpp)
# LICENSE
Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.
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