juncmut

The function for analyzing splicing junction associated variant (generated by STAR or bamTojunction, .SJ.out.tab files )

Dependency

Binary programs

samtools, bedtools

Python

pysam, edlib, bio

Install

Download this repository and run prep.sh

pip install git+https://github.com/ncc-gap/juncmut.git

cd db
bash prep.sh
cd ..

Commands

detect

juncmut detect [-h] 
               [--control_file [CONTROL_FILE [CONTROL_FILE ...]]]
               [--read_num_thres READ_NUM_THRES]
               [--freq_thres FREQ_THRES]
               [--mut_num_thres MUT_NUM_THRES]
               [--mut_freq_thres MUT_FREQ_THRES]
               [--support_read_rmdup_thres SUPPORT_READ_RMDUP_THRES]
               [--debug]
               input.SJ.out.tab input.bam juncmut.txt reference.fa gencode.v46.basic.annotation.gtf.gz

positional arguments:
  input.SJ.out.tab      Input splice junctions generated by STAR
  input.bam             Input RNA bam file
  juncmut.txt           Output file
  reference.fa          Reference genome
  gencode.v46.basic.annotation.gtf.gz
                        GENCODE gene file

optional arguments:
  -h, --help            show this help message and exit
  --control_file [CONTROL_FILE [CONTROL_FILE ...]]
                        Control data created by merge_control (default: None)
  --read_num_thres READ_NUM_THRES
                        Splicing junctions with reads >= read_num_thres is saved (default: 3)
  --freq_thres FREQ_THRES
                        Splicing junctions with reads >= freq_thres is saved (default: 0.05)
  --mut_num_thres MUT_NUM_THRES
                        A mutation with mutation alleles >= mut_num_thres is a true candidate (default: 1)
  --mut_freq_thres MUT_FREQ_THRES
                        A mutation with frequency >= mut_freq_thres is a true candidate (default: 0.05)
  --support_read_rmdup_thres SUPPORT_READ_RMDUP_THRES
                        A mutation with mutation alleles >= mut_num_thres is a true candidate (default: 2)
  --debug               True keeps the intermediate files.

filt_bam

usage: juncmut filt_bam [-h] juncmut.txt input.bam juncmut.filt.bam wgEncodeGencode.txt.gz

positional arguments:
  juncmut.txt           juncmut.txt
  input.bam             Input RNA bam file
  juncmut.filt.bam      Output bam file
  wgEncodeGencode.txt.gz
                        GENCODE gene file

optional arguments:
  -h, --help            show this help message and exit

sjclass

usage: juncmut sjclass [-h] [--gencode gencode.v46.basic.annotation.gtf.gz] [--depth_th depth_th] [--debug]
                       juncmut.annot.txt juncmut.annot.sjclass.txt juncmut.filt.bam input.SJ.out.tab reference.fa

positional arguments:
  juncmut.annot.txt     Input file(such as file generated by juncmut
  juncmut.annot.sjclass.txt
                        Output classified file
  juncmut.filt.bam      Input RNA bam file
  input.SJ.out.tab      Input splice junctions generated by STAR
  reference.fa          Reference genome

optional arguments:
  -h, --help            show this help message and exit
  --gencode gencode.v46.basic.annotation.gtf.gz
                        GENCODE gene file
  --depth_th depth_th   Depth in the intron for classification.
  --debug               keep temporary files.

alu

usage: juncmut alu [-h] [--alu {Alu_Funakoshi,AluJ0,AluJ0pA,AluYb8pA}] [--debug]
                   juncmut.sjclass.txt juncmut.sjclass.alu.txt rmsk_sine.bed reference.fa

positional arguments:
  juncmut.sjclass.txt   Input file (generated by juncmut sjclass
  juncmut.sjclass.alu.txt
                        Output mapped alu file
  rmsk_sine.bed         Input rmsk_sine.bed (db/rmsk_sine.bed)
  reference.fa          Reference genome

optional arguments:
  -h, --help            show this help message and exit
  --alu {Alu_Funakoshi,AluJ0,AluJ0pA,AluYb8pA}
                        choice alu reference
  --debug               keep temporary files.

annot

usage: juncmut annot [-h] [--acmg_file ACMG_SF_v3.2.txt] [--cgc_file CancerGeneSensus_GRCh38_v97.txt] [--cgd_file CGD.txt] [--clinvar_file clinvar.vcf.gz]
                     [--clinvar_star234_file clinvar_star234_gene.txt] [--dosage_sensitivity_file clingen_dosage_sensitivity_230105.proc.txt]
                     [--gnomad gnomad.genomes.r3.0.sites.vcf.bgz] [--pancan_file PANAtlas_CellTableS1.txt] [--debug]
                     juncmut.txt juncmut.annot.txt reference.fa

positional arguments:
  juncmut.txt           Input file (such as juncmut.txt generated by juncmut)
  juncmut.annot.txt     Output annotated file
  reference.fa          Reference genome

optional arguments:
  -h, --help            show this help message and exit
  --acmg_file ACMG_SF_v3.2.txt
  --cgc_file CancerGeneSensus_GRCh38_v97.txt
  --cgd_file CGD.txt
  --clinvar_file clinvar.vcf.gz
  --clinvar_star234_file clinvar_star234_gene.txt
  --dosage_sensitivity_file clingen_dosage_sensitivity_230105.proc.txt
  --gnomad gnomad.genomes.r3.0.sites.vcf.bgz
  --pancan_file PANAtlas_CellTableS1.txt
  --debug               True keeps the intermediate files.

filt

usage: juncmut filt [-h] juncmut.annot.txt juncmut.annot.filt.txt

positional arguments:
  juncmut.annot.txt     Input file(such as juncmut.txt generated by juncmut)
  juncmut.annot.filt.txt
                        Output filted file

optional arguments:
  -h, --help            show this help message and exit

Tutorial

See this page