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HAPLRT(1) hapLrt (VCF genotype) HAPLRT(1) NAME hapLrt SYNOPSIS hapLRT -target 0,1,2,3,4,5,6,7 -background 11,12,13,16,17,19,22 -type GP -file my.vcf DESCRIPTION HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribution. The sign denotes if the target has longer haplotypes (1) or the background (-1). OPTIONS Output : 4 columns : 1. seqid 2. position 3. mean target haplotype length 4. mean background haplotype length 5. p-value from LRT 6. sign required: t,target -- argument: a zero base comma separated list of target individuals corresponding to VCF columns required: b,background -- argument: a zero base comma separated list of background individuals corresponding to VCF columns required: f,file -- argument: a properly formatted phased VCF file required: y,type -- argument: type of genotype likelihood: PL, GL, GT or GP optional: r,region -- argument: a genomic range to calculate **hapLrt** on in the format : "seqid:start-end" or "seqid" Type: genotype 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. hapLrt (vcflib) HAPLRT(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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