chimera_utils

Introduction

This is a suite of tools for processing chimeric reads generated at a STAR alignment step (Chimeric.out.sam files).

Dependency

Python

pysam, annot_utils, fusionfusion

Software

htslib, bedtools

Install

pip install chimera_utils

Alternatively you can download from the source code:

wget https://github.com/friend1ws/chimera_utils/archive/v0.5.0.tar.gz
tar zxvf v0.6.0.tar.gz
cd chimera_utils-0.6.0
python setup.py build install

For the last command, you may need to add --user if using a shared computing cluster.

Commands

count

Count supporting read pairs for each chimera junction

chimera_utils count [-h] [--abnormal_insert_size ABNORMAL_INSERT_SIZE]
                          [--min_major_clipping_size MIN_MAJOR_CLIPPING_SIZE]
                          [--min_read_pair_num MIN_READ_PAIR_NUM]
                          [--min_cover_size MIN_COVER_SIZE]
                          [--anchor_size_thres ANCHOR_SIZE_THRES]
                          [--min_chimeric_size MIN_CHIMERIC_SIZE] [--debug]
                          Chimeric.out.sam output_file

merge_control

Merge chimeric junction cout file (generated by count command) of control data (typically) for later filtering

chimera_utils merge_control [-h] chimeric_count_list.txt output_file

associate

Associate chimeric junctions with the output of GenomonSV

chimera_utils associate [-h] [--margin MARGIN]
                               [--sv_margin_major SV_MARGIN_MAJOR]
                               [--sv_margin_minor SV_MARGIN_MINOR]
                               [--genome_id {hg19,hg38,mm10}] [--grc]
                               [--debug]
                               chimera.txt genomonSV.result.txt output.txt