Generates phased haplotypes from multisample Battenberg runs

Source: R/haplotype_external.R

Generates phased haplotypes from multisample Battenberg runs

get_multisample_phasing(
  chrom,
  bbphasingprefixes,
  maxlag = 90,
  relative_weight_balanced = 0.25,
  outprefix
)

Arguments

chrom

chromosome for which to obtain haplotypes

bbphasingprefixes

Vector containing prefixes of the Battenberg_phased_chr files for the multiple samples

maxlag

Maximal number of upstream SNPs used to inform the haplotype at another SNPs

relative_weight_balanced

Relative weight to give to haplotype info from a sample without allelic imbalance in the region (default 0.25)

outprefix

Prefix of the ouput multisample phasing files

Author

jdemeul