butyuhao/mhaptools

The homepage: https://jiantaoshi.github.io/mHap/index.html

The PDF file of the paper: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab458/6305824

If you find mHapTools is helpful, please cite:

@article{zhang2021dna,
  title={The DNA methylation haplotype (mHap) format and mHapTools},
  author={Zhang, Zhiqiang and Dan, Yuhao and Xu, Yaochen and Zhang, Jiarui and Zheng, Xiaoqi and Shi, Jiantao},
  journal={Bioinformatics},
  year={2021}
}

Build example

cd mHapTools
cd htslib-1.10.2
./configure --prefix=`pwd`
make
make install
cd ..
g++ -o mhaptools  haptk.cpp convert.cpp mhap.cpp merge.cpp beta.cpp summary.cpp utils.cpp -I ./htslib-1.10.2/htslib -I ./include  -L ./htslib-1.10.2/ -lhts -std=c++11
export LD_LIBRARY_PATH=`pwd`/htslib-1.10.2/lib

Commands

• convert

Convert SAM/BAM format file to mHap format file. It takes an indexed Bisulfite-seq BAM and CpGs position files as inputs to extract DNA methylation haplotypes.

• merge

Merge multiple sorted mHap files, produce a single sorted mHap file.

• beta

Output summary of CpG site-level methylation from mHap files. It is similar to Bismark DNA methylation caller but uses mHap as inputs.

• summary

Computes the total number of reads, methylated CpG sites, total CpG sites, DNA methylation discordant reads, methylated reads for given genomic regions or genome wide.

Details

convert

• -i input file, SAM/BAM format, should be sorted by samtools.
• -n non-directional, do not group results by the direction of reads.
• -b bed file, one query region per line.
• -c CpG file, gz format.
• -r region. chr1:2000-200000
• -m sequencing mode. ( TAPS | BS (default) )
• -o output filename. (default: out.mhap.gz)

merge

• -i input file, multiple .mhap.gz files to merge.
• -c CpG file, gz format.
• -o output filename. (default: merge.mhap.gz)

beta

• -i input file, .mhap.gz format.
• -c CpG file, gz format.
• -o output filename. (default: beta.txt)
• -s group results by the direction of mHap reads.
• -b bed file, one query region per line.

summary

• -i input file, mhap.gz format.

//Generate index for .mhap.gz file
tabix -b 2 -e 3 file.mhap.gz

• -c CpG file, gz format.
• -b bed file of query regions.
• -r query region, e.g. chr1:2000-20000.
• -o output fiename. (summary.txt | summary_genome_wide.txt)
• -s group results by the direction of mHap reads.
• -g get genome-wide result.

mhaptools's Issues

could mhaptools convert bam generated by bwa-meth to mhapfile ?

could mhaptools convert bam generated by bwa-meth to mhapfile ?

The using requirement of mHapTools

Hi, I have a question about the tool mHapTools. I used the alignment results to do methylation haplotypes by mHapTools, but I can't extract the methylation haplotypes from the alignment result, I would like to know if mHaplotype only process the alignment results generated by BISMARK or BSMAP.