Haplotyping for different sample types (individual or pool)

Individual and pooled samples are different in two major ways;

• In individuals, low frequency haplotypes (<5%) are generally noise and need to be removed from the data. In pools on the other hand it is hard to discriminate between noise and low frequency alleles.

• In individuals and pools haplotype frequencies are calculated. In addition, in individuals these haplotypes can be converted into discrete haplotype calls, which can be either dominant (0/1) or dosed (0/1/2(/3/4)).

Therefore these two sample types are separately discussed.

It is not necessary to define your sample type in the program/command line.

Contents:

• Individuals
  • Step 3: Filtering haplotypes and calculating haplotype frequencies
  • Step 4: Transforming haplotype frequencies to discrete calls in individuals
  • Output
  • Code
• Pools
  • Step 3: Filtering haplotypes and calculating haplotype frequencies
  • Output
  • Code