Provided by: libvcflib-tools_1.0.3+dfsg-1_amd64 bug

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 2011-2022 (C) Erik Garrison and vcflib contributors.  MIT licensed.


AUTHORS
       Erik Garrison and vcflib contributors.