ncc-gap/ModbamETLTools

Modbam ETL tools

Modbam ETL tools

Intoroduction

This script can output the fastq file and mm/ml tag information separately from the bam file. After mapping the output fastq file with any mapper, the process of merging mm/ml tag information is executed.

Setup

Requirement

• Docker

For use with Docker

git clone https://github.com/ncc-ccat-gap/ModbamETLTools.git
docker build ModbamETLTools/Dockerfile -t modbametltools:0.2.0
docker run -it modbametltools:0.2.0 /bin/bash

• When starting the container, please mount the input/output destination according to the environment.
• If you also have a singularity environment, you can also create a .sif to use.

singularity build modbamETLtools-0.2.0.sif docker-daemon://modbametltools:0.2.0

Without Docker

• It can be used even if you do not have a Docker environment.
• In that case, please set up the following environment

Requirement

• Python 3.8.x
• pysam 0.20.0
• modbam2bed v0.6.3

setup

git clone https://github.com/ncc-ccat-gap/ModbamETLTools.git
cd ModbamETLTools
python setup.py install

caution

• <exec_bam_to_bed.sh> is a script created with the assumption that it will run in a Docker environment.
  • The modbam2bed path in the <exec_bam_to_bed.sh> file should be rewritten according to your environment

Usage

Export fastq and MM/ML tag info from bam

export_tag -i <input_bam_file> [-o output_file_path] [--no_fastq]

Merge MM/ML tag info into the bam file

merge_tag -i <input_bam_file> -t <input_mm/ml_tag_file> [-o output_file_path] [--no_sort] [--threads <int>]

Export bam file split by HP tag

split_bam -i <input_bam_file> [-o output_file_path]

Convert modified base BAM file to BED file

cd ModbamETLTools/scripts/etl_tools
bash exec_bam_to_bed.sh <input_bam_file> <fasta_file> <threads>

How to Use

• Example: qsub option for thread 8 is as follows
  • def_slot 4
  • s_vmem 4G

(1) Output tag information and fastq file from bam file.

export_tag -i /home/user/sample1.bam

• If option '-o' is omitted, the output is current.
• If '--no_fastq' is given as an argument, the .fastq file is not output

Output

• sample1_export.fastq
• sample1_export_taginfo.txt

(2) Tag information to bam files processed by any mapper.

merge_tag -i /home/user/sample2.bam -t /home/user/sample1_export_taginfo.txt

• If option '-o' is omitted, the output is current.
• If '--no_sort' is given as an argument, the sorting process is skipped.
• You can specify the number of cores to process by giving '--threads' as an argument.(default:8)

Output

• sample2_merge_tags.bam
• sample2_merge_tags_sorted.bam
• sample2_merge_tags_sorted.bam.bai

(3) Split bam with haplotype tag.

split_bam -i /home/user/sample2_merge_tags_sorted.bam

• If option '-o' is omitted, the output is current.

Output

• sample2_merge_HP_none.bam
• sample2_merge_HP2.bam
• sample2_merge_HP1.bam
• sample2_merge_HP1.bam.bai
• sample2_merge_HP2.bam.bai
• sample2_merge_HP_none.bam.bai

(4)Convert modified base BAM file to BED file

cd ModbamETLTools/scripts/etl_tools
bash exec_bam_to_bed.sh /home/user/sample2_merge_HP_none.bam /home/user/reference.fasta 8

Output

• sample2_merge_HP_none_mod-counts.cpg.acc.bed

• sample2_merge_HP_none.bed

  • '*-counts.cpg.acc.bed' : strands are aggregated