Ncsv is a structural variant calling, annotation and filting software. It uses Split Reads, Single Unmap and Discordant Pair to discover the structural variants throughout the genome.
git clone https://github.com/GenePlus/ncsv.git --recursive
sh ncsv/inst.sh #compile (cd ncsv/extension/sv_helper && python setup.py build_ext --inplace #generate so file)
Ncsv use a run_sv.py file as a start step.
python2 bin/run_sv.py [-h]
[-S SAMPLE] -t TMP -r REF -H HOTREGION
[-w BWA] [-s SAMTOOLS] [-n NUMTHREADS]
[-d] [--bamstat BAMSTAT] [--hotsv HOTSV]
[-c CTRLOUT] outfile bamt [bamn]
positional arguments:
outfile output file, csv format
bamt bam to do sv analysis
bamn ctrl bam
optional arguments:
-h, --help show this help message and exit
-t TMP, --tmp TMP tmp file path
-r REF, --ref REF reference genome, it should be same with the one used by bam
-H HOTREGION, --hotregion HOTREGION hot region file, generated by sv flow helper script
-w BWA, --bwa BWA default is bwa
-s SAMTOOLS, --samtools SAMTOOLS default is samtools
-n NUMTHREADS, --numthreads NUMTHREADS num of threads, default is 4
-c CTRLOUT, --ctrlout CTRLOUT norm sv output file, csv format
-S SAMPLE, --sample SAMPLE sample name, set None to infer it from bam path
-d, --debug open debug logging
--bamstat BAMSTAT bam stat file, isize could be abstracted from it
--hotsv HOTSV the bed file as hot sv region. WARNING: only analysis the sv inner these region
More docs refers to ncsv on read the docs.
ncsv source code is provided under the Apache License 2.0. ncsv includes several third party packages provided under other open source licenses, please see COPYRIGHT.txt for additional details. Specially, this program use svaba to process local assembly.