/mHapTools

Primary LanguageCOtherNOASSERTION

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
  • -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 -p bed 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.