Description

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

0 ()

1 ()

2 ()

0 ()

1 ()

0 ()

1 ()

2 ()

0 ()

1 ()

2 ()

stutter_in (file)

Optional input file containing stutter models. Stutter models in this file will be used to genotype STRs. By default, HipSTR learns stutter models via the EM algorithm.

*.txt

fam (file)

Optional FAM file (PLINK sample information file) containing pedigree information for samples of interest. The pedigree information is used to filter SNPs prior to phasing STRs. By default, all SNPs are used.

*.fam

hap_chr_file (file)

Optional file containing chromosomes to treat as haploid, one per line

*.txt

save_log (boolean)

Whether to output the log information to the file (Default = Standard error)

save_viz (boolean)

Whether to output a file of each locus' alignments for visualization with VizAln or VizAlnPdf

save_stutter (boolean)

Whether to output stutter models learned by the EM algorithm to the file

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

hipstr Documentation

Haplotype inference and phasing for short tandem repeats

https://github.com/tfwillems/HipSTRdoi: 10.1038/nmeth.4267License: GPL-2.0
Authors