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Python tools for processing chimeric reads and lists of gene fusions.

Project description


License: GPL v3 Build Status


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



pysam, annot_utils, fusionfusion


htslib, bedtools


pip install chimera_utils

Alternatively you can download from the source code:

tar zxvf v0.6.0.tar.gz
cd chimera_utils-0.6.0
python build install

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



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 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 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]
                               chimera.txt genomonSV.result.txt output.txt

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