gt: Facilities for essential tasks in R

Description Usage Arguments Details Value Author(s) Examples

Adjust Ancentral/Derived Alleles According to Reference

shapeit_set_ancestor(
  shapeit,
 
    ref = "~/cmcouto.silva@usp.br/lab_files/datasets/Reference_annotation/1000g_ancestor/human_ancestor_GRCh37_e59/",
  out
)

`shapeit`	Scalar character with the name of the dataset file on Shapeit format without extension (.haps/.sample).
`ref`	Scalar character with the path of the reference fasta files (1000G).
`out`	Scalar character with desired name for the output file (without extension).

Freely download of 1000 Genomes Ancestor alleles available at: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/

Dataset with adjusted ancestral/derived alleles (.haps and .sample files).

Cainã Max Couto-Silva

## Not run: 
haps <- "dataset/my_phased_dataset"
ref <- "path_to_fasta_files/"
out <- "out_folder/phased_data_with_fixed_ancestor"

set_anc_alleles(sfile, ref, out)

## End(Not run)