/ob_utils

Primary LanguagePythonMIT LicenseMIT

ob_utils

Merge SV results detected by multiple tools.

Dependency

Python

Python (>=3.7)

Software

bedtools, sv_utils(>=0.6.1), pysam

Install

python3 setup.py install

Commands

ob_utils manta_sv [-h] --in_manta_sv IN_MANTA_SV --output OUTPUT
                         [--margin MARGIN] [--f_grc]

ob_utils gridss_sv [-h] --in_gridss_sv IN_GRIDSS_SV --output OUTPUT
                          [--margin MARGIN] [--f_grc]

ob_utils svaba_sv [-h] --in_svaba_sv IN_SVABA_SV --in_svaba_indel
                         IN_SVABA_INDEL --output OUTPUT [--margin MARGIN]
                         [--f_grc] [--f_germ]
                         [--normal_max_variant NORMAL_MAX_VARIANT]
                         [--tumor_min_variant TUMOR_MIN_VARIANT]
                         [--normal_min_depth NORMAL_MIN_DEPTH]
                         [--tumor_min_depth TUMOR_MIN_DEPTH]
                         [--min_del_size MIN_DEL_SIZE]
                         [--min_ins_size MIN_INS_SIZE]

ob_utils genomon_sv [-h] --in_genomon_sv IN_GENOMON_SV --output OUTPUT
                           [--margin MARGIN] [--f_grc]

ob_utils merge_sv [-h] --in_genomonsv IN_GENOMONSV --in_manta IN_MANTA
                         --in_svaba IN_SVABA --in_gridss IN_GRIDSS --output
                         OUTPUT [--margin MARGIN] [--f_grc] [--f_germ]
                         --simple_repeat_file SIMPLE_REPEAT_FILE --reference
                         REFERENCE [--genome_id {hg19,hg38}]

You can check the manual by typing

ob_utils manta_sv -h

ob_utils merge_sv -h

Results

The primary result is {OUTPUT}