IHS(1) iHS (VCF statistics) IHS(1) NAME iHS SYNOPSIS iHS -target 0,1,2,3,4,5,6,7 -file my.phased.vcf -region chr1:1-1000 > STD- OUT 2> STDERR DESCRIPTION iHS calculates the integrated haplotype score which measures the relative decay of extended haplotype homozygosity (EHH) for the reference and alter- native 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 2011-2025 (C) Erik Garrison and vcflib contributors. MIT li- censed. Copyright 2020-2025 (C) Pjotr Prins. AUTHORS Erik Garrison and vcflib contributors. iHS (vcflib) IHS(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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