qp_genotypes: Quasi-phased genotypes
In surh/HMVAR: Human Microbiome Variant Analysis in R

From allele frequency data in the format of midas_merge.py snps it determines which samples and which positions in each sample are quasi-phaseable and makes the corresponding genotype calls.

qp_genotypes(
  midas_dir,
  midas_dat,
  map = NULL,
  min_depth = 5,
  min_snv_prop = 0.8,
  maf_thres = 0.2
)

`midas_dir`	Directory with outptu from mdas_merge.py snps. Either this or midas_dat needs to be provided.
`midas_dat`	A list with info, freq, and depth elements corresponding to the result of read_midas_data. Either this or midas_dir needs to be provided
`map`	A data table associating samples in the MIDAS otput to groups. It must have an 'sample' and a 'Group' column. Only used if midas_dat was passed and only samples in map are processed.
`min_depth`	Minimum sequence depth at a given sample and position to be abele to call a gnotype
`min_snv_prop`	Minimum proportion of SNVs in a sample, among SNVs that pass the min_depth filter, that pass the maf_thres filter. Samples that have a smaller proportion of SNVs passing this condition are considered non-quasi-phaseable and genotype calls are not made.
`maf_thres`	A value in the range [0, 0.5]. SNVs are only considered quasi-phaseable if their frequency (f) fullfills f <= maf_thres \| f >= 1 - maf_thres, and if they are in a quasi-phaseable sample. SNVs in quasi-phaseable samples, that do not pass the maf_thres or min_depth filters are considered missing data.