sv_utils

utility scripts for processing and summarizing Genomon-SV results

Dependency

Python

Python (>= 2.7), genomon_sv (for merge_control, realign and primer), pysam, primer3-py (for primer) packages

Software

tabix, bgzip, blat (for realign)

Install

pip install sv_utils

Alternatively, if you want to install from the source code:

git clone https://github.com/friend1ws/sv_utils.git
cd sv_utils
pip install .

Commands

For detailed description on each option, please consult the help for each command

count

Summarize the frequency of each variant type (deletion, tandem_duplication, inversion and translocation) for each sample

sv_utils count [-h] [--inseq] result_list.txt output.txt

gene_summary

Summarize the frequency of each variant type (deletion, tandem_duplication, inversion, translocation) for each cancer gene

gene_summary [-h] --cancer_gene_list cancer_gene_list
                             [--inframe_info]
                             result_list.txt output.txt

For the --cancer_gene_list argument, the CancerGeneSummary/CancerGeneSummary.proc.txt in the cancer_gene_db repository or its variation could be used.

filter

Filter out GenomonSV results outside specified conditions

sv_utils filter [-h] [--genome_id {hg19,hg38,mm10}] [--grc]
                       [--max_minus_log_fisher_pvalue MAX_MINUS_LOG_FISHER_PVALUE]
                       [--min_tumor_allele_freq MIN_TUMOR_ALLELE_FREQ]
                       [--max_control_allele_freq MAX_CONTROL_ALLELE_FREQ]
                       [--max_control_variant_read_pair MAX_CONTROL_VARIANT_READ_PAIR]
                       [--control_depth_thres CONTROL_DEPTH_THRES]
                       [--min_overhang_size MIN_OVERHANG_SIZE]
                       [--inversion_size_thres INVERSION_SIZE_THRES]
                       [--max_variant_size MAX_VARIANT_SIZE]
                       [--pooled_control_file POOLED_CONTROL_FILE]
                       [--pooled_control_num_thres POOLED_CONTROL_NUM_THRES]
                       [--simple_repeat_file SIMPLE_REPEAT_FILE]
                       [--remove_rna_junction]
                       genomonSV.result.txt output.txt

annotation

Annotate GenomonSV results

sv_utils annotation [-h] [--genome_id {hg19,hg38,mm10}] [--grc]
                           [--re_gene_annotation] [--closest_exon]
                           [--closest_coding] [--coding_info]
                           [--fusion_list FUSION_LIST]
                           genomonSV.result.txt output.txt

For the --fusion_list argument, the fusion_db.txt file in the fusion_db repository cound be used.

mutation

Add somatic SNVs and short indels to the GenomonSV results

sv_utils mutation [-h] --reference reference.fa
                         genomonSV.result.txt genomon_mutation.result.txt
                         output.txt

concentrate

List up concentrated structural variations

sv_utils concentrate [-h] [--set_count set_count]
                            [--set_margin set_margin]
                            result_list.txt output.txt

merge_control

Merge, compress and index the lists of GenomonSV results

sv_utils merge_control [-h] result_list.txt merge_control.bedpe.gz

realign

Realign short reads around the structural variation candidates for mainly validation purpose

sv_utils realign [-h] --reference reference.fa --tumor_bam tumor.bam
                        [--control_bam control.bam]
                        genomonSV.result.txt output.txt

primer

Generate primer sequence for mainly PCR validation

sv_utils primer [-h] --reference reference.fa
                       genomonSV.result.txt output.txt

format

convert to vcf format for short deletions and tandem duplications

sv_utils format [-h] --reference reference.fa [--format {vcf}]
                       [--max_size_thres MAX_SIZE_THRES]
                       genomonSV.result.txt output.txt

nonB_DB

Get distance to nonB_DB annotated region for each SV candidate

sv_utils nonB_DB [-h] --nonB_DB nonB_DB.bed.gz
                        genomonSV.result.txt output.txt

For the --nonB_DB argument, the nonB_DB.bed.gz in the nonB_DB repository could be used.

RSS

Check recombination signal sequence motif near breakpoints

sv_utils RSS [-h] --reference reference.fa [--check_size CHECK_SIZE]
                    genomonSV.result.txt output.txt

AID

Check AID motif (CG, WGCW) near breakpoints

sv_utils AID [-h] --reference reference.fa [--check_size CHECK_SIZE]
                    genomonSV.result.txt output.txt

ken0-1n/sv_utils