Skip to content
No description, website, or topics provided.
Python Shell
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
example
scripts
README.md
Snakefile

README.md

Requirements

- Snakemake: https://snakemake.readthedocs.io/en/stable/
- Wext: https://github.com/raphael-group/wext

Example

Run example as: snakemake --configfile example/config --cores 8

Usage

Input file

  1. Data file. Comma-separated file, with one line per variant with the following columns:
  • loc: The genomic position of the variant
  • allele_a, allele_b
  • a_i, b_i: For each sample i, the count of the a allele and b allele respectively.

Example:

loc,allele_a,allele_b,a_0,b_0,a_1,b_1,a_2,b_2,a_3,b_3,a_4,b_4,a_5,b_5,a_6,b_6,a_7,b_7,a_8,b_8
1897,G,A,5,0,0,0,0,0,0,0,0,0,4,0,1,0,2,0
11754,C,T,1,0,0,0,0,0,0,3,0,0,4,0,8,1,0,0
13656,A,G,2,0,4,0,2,2,0,0,0,0,0,0,4,0,0,0
  1. Config file. YAML formatted file with the following entries:
  • outdir: output directory
  • cutoff: cutoff parameter(s)

Output file

  1. hapcut_input_f/mda_fragments.{CUTOFF}.txt Output fragments in hapcut2 format
You can’t perform that action at this time.