mMHtyper is an end-to-end pipeline for recognizing the multi-SNP microhaplotypes in Nanopore sequencing data. If you have more than two SNPs to recognize microhaplotypes, you can choose mMHtyper not MHtyper.
The raw reads were filtered by NanoFilt, you can set the Q-value and the length according to your work.
To get the high-quality alignments, we filtered the ".bam" files by setting the MAPQ>50 and Flag =16 & 0.
1. The filtered ".bam" files and a bed file were as the input of mMHtyper, the header of bed file as below table.
| MiniHap name | chromosome | db SNP | Position (GRCh38) | REF | ALT |
|---|
MiniHap name: The name of your multi-SNP microhaplotypes.
Chromosome: The name of Chromosome.
db SNP: The ID of SNP.
Position (GRCh38):The positions of SNP in GRCh38.
REF: The base of SNP in GRCh38.
ALT: The alleles of SNP.
2. The mMHtyper can create the "Phasing.txt", the header of it as below table.
| chr | pos | REF | sample | db SNP | genotypes | depth | phase1 | phase2 |
|---|
chr: The name of Chromosome.
pos: The positions of SNP in GRCh38.
REF: The base of SNP in GRCh38.
sample: The name of your multi-SNP microhaplotypes.
db SNP: The ID of SNP.
genotypes: The genotypes of SNP.
depth: The depth of SNP, the max depth is 10000.
phase1: The haplotype 1 of SNP.
phase2: The haplotype 2 of SNP.
conda create -n mMHtyper
conda activate mMHtyper
conda config --add channels bioconda
conda config --add channels
conda install --yes --file requirements.txt
git clone https://github.com/willow2333/mMHtyper.git
cd mMHtyper
python mMHtyper.py --h
usage: Phasing.py [-h] [--sampledir SAMPLEDIR] [--ref REF] [--bed BED]
optional arguments:
-h, --help show this help message and exit
--sampledir SAMPLEDIR
The absolute path of fastq files, the fastq files need
be gzip and named *.fq.gz
--ref REF The absolute path of reference file
--bed BED The absolute path of bed file
python mMHtyper.py --sampledir {path} --ref hg38.fa --bed XX.bed
© 2023 by Yiping Hou (forensic@scu.edu.cn), Zheng Wang (wangzhengtim@scu.edu.cn), Liu Qin (ql_willow@163.com)