iHS

       Erik Garrison and vcflib contributors.

iHS (vcflib)                                                                                              IHS(1)

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

0      Success

       not0  Failure

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

iHS

              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

vcflib(1)

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