LR_Filter

The LR_Filter provides information for filtering the false Structural Variations (SVs, VCF format) based on a long-read mapping file (BAM format). This is developed for ETCHING project.

Requirements

The LR_Filer was written by Python 3 a along with some Python modules. The required modules are as follows.

sys
argparse
math
re
os
pickle
pysam
numpy
queue
threading
multiprocessing

If you want to install required modules, refer to the command below


pip install {"module_name"}

Usages

python LR_Filter.py -h


usage: LR-Filter.v0.4.py [-h] [-i INPUT_VCF] [-t TARGET_TYPE] [-lbt LONG_BAM_T] [-lbn LONG_BAM_N] [-rf REFERENCE_SEQ] [-c CPUS] [-tr TARGET_RANGE] [-o OUTNAME]

LR_Filter is SV filtering tool using long-read BAM file

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_VCF, --input_VCF INPUT_VCF
                        The input VCF file by short-read SV caller, etc ETCHING, Lumpy, Delly ...
  -t TARGET_TYPE, --target_type TARGET_TYPE
                        The target SV type, etc DEL, DUP, INV, or TRA
  -lbt LONG_BAM_T, --long_bam_t LONG_BAM_T
                        A tumor long-read mapping sorted BAM file by Minimap2 or NGMLR
  -lbn LONG_BAM_N, --long_bam_n LONG_BAM_N
                        A normal long-read mapping sorted BAM file by Minimap2 or NGMLR
  -rf REFERENCE_SEQ, --reference_seq REFERENCE_SEQ
                        The reference fasta file, etc hg19 or hg38
  -c CPUS,           --cpus CPUS, default: 1 cpu
                        Set the number of CPUs, this option is for multi-processing
  -tr TARGET_RANGE, --target_range TARGET_RANGE, default: 500bp
                        Set the range of the SV BreakPoints (BPs) for verifying by long-reads
  -o OUTNAME, --outname OUTNAME
                        Output name

Example

LR_Filter requires long-read BAM file as primary input and two modes are currently available.

Somatic SV mode: this mode requires both tumor-normal long-read mapped BAM files
General SV mode: in this mode, only a single long-read mapped BAM file is required

Somatic SV mode


python LR_Filter.py -i {input_VCF_file} -t {DEL} -lbt {tumor_long_read_sorted_BAM_file} -lbn {normal_long_read_sorted_BAM_file} \
                    -rf {hg19.fa} -c {1} -tr {500} -o {test}

General SV mode