Reading Haplotype Data

Louis Aslett & Ryan Christ

2025-07-28

kalis calculates pairwise genetic distances at loci of interest for a set of phased haplotypes stored in a L x N matrix H where H[l,i] = 1 if haplotype i carries the alternative allele at locus l and H[l,i] = 0 if it carries the reference allele. For efficiency kalis internally must load and store H as a matrix of bits.

For all of the data input types below, it assumed that the haplotypes have already been phased, as required to run kalis.

Reading from BCF/VCF

To read phased haplotypes stored in a compressed or uncompressed BCF or VCF, the file must first be converted to HAP/SAMPLE/LEGEND format. For example, for a given compressed VCF, we simply call bcftools as follows.

bcftools convert -h my.vcf.gz

Then, from R, we read in the haplotypes by calling

require(kalis)
CacheHaplotypes("my.hap.gz")

See http://samtools.github.io/bcftools/bcftools.html#convert for more details.

For increased reading efficiency CacheHaplotypes look will look for the my.legend file that was produced by bcftools in the same directory as my.hap.gz so its worthwhile keeping the .legend files.

bcftools can read from many different formats into BCF/VCF, making it an easy tool for conversion into HAP/SAMPLE/LEGEND format.

kalis http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/

ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.hap.gz