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)

OTHER

LICENSE

Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS
Erik Garrison and vcflib contributors.