glhap

DOCUMENTATION

This software provedis you a way to calculate haplogroups depending of genotype likelihood

Dependencies

C:

• htslib

https://github.com/samtools/htslib

Python

• anytree 2.8.0
• numpy 1.17.4
• pysam 0.18.0

Also you may need PhyloTree.org-parser for making haplogrep tree in json format https://github.com/alexeyshmelev/PhyloTree.org-parser/tree/main

How to run:

Calculate haplogroups with samtools likelihood model:

glhap.py

you can simply use

./glhap.py array/array.json {vcf_file}.vcf

array.json is provided phylotree17 in json.

The program will produce top 10 haplogroups with their log-likelihood

Calculate haplogroups with hamming distance model:

HOW TO USE g++ hamgrep.c -lhts -o hamgrep ./hamgrep f1.fa

• f1.fa is fasta file for called dna YOU MUST HAVE A "filelist.txt" FILE IN FOLDER WITH EXECUTIVE FILE WHERE LIST OF FASTA FILES MUST BE WRITTEN MUST BE WRITTEN

Calculate haplogroups with gatk likelihood model:

g++ hamgrep.c -lhts -o hamgrep

./hamgrep {piliup}.pileup

{pileup}.pileup is pileup file, you can get it with

samtools mpileup -f ref.fa -B -o pileup.pileup in.bam

you must have A "filelist.txt" file in folder with executive file where list of fasta files must be written.

gl_cont

This software provides you to estimate contamination in DNA based on quality score.

Dependencies

• simlord 1.0.4
• numpy 1.22.3
• tqdm 4.64.0
• biopython 1.78
• cython 0.29.30
• pysam 0.19.1 Picard GATK

How to run:

for first use you should type python setup.pu build_ext --inplace

then

./gl_cont.py bam.bam ref.ref contaminants.fa nIter where nIter - number of iteration for MCMC

Simulate data

---

You may generate data with script based on simlord

python contamsim.py hap1.fa prop1 [...] hapn.fa propn prop1 is number of reads divided by 100000