Base/Prime Editor Induced DNA Off-target site identification Unified toolkit
Version: 1.0.0
About the name: "BeiDou" is also the name of China's navigation satellite system
Authors: Wei Xue(xuewei@picb.ac.cn), Zhi-Can Fu(fuzhican@picb.ac.cn) and Li Yang (liyang@picb.ac.cn)
Maintainer: Zhi-Can Fu(fuzhican@picb.ac.cn)
- Software
- bwa (version 0.7.17-r1188)
- perl (version 5.26.2)
- samtools (version 1.9)
- bedtools (version 2.28.0)
- picard (version 2.21.2)
- bamtools (version 2.5.1)
- bcftools (version 1.9)
- GATK (version 4.1.3.0-0)
- lofreq (version 2.1.3.1)
- Strelka2 (version 2.9.10)
- Scalpel (version 0.5.4)
- Manta (version 1.6.0)
- GNU Parallel (version 20200722)
- R (version 3.5.1)
- reference sequences
- vcfs for GATK BaseRecalibrator
- NCBI_dbSNP_all_hg38.vcf.gz|EVA_SNP_all_mm10.vcf.gz (Very importantly, chromosome names in the annotations GTF file have to match chromosome names in the FASTA genome sequence files)
- vcfs for GATK VariantRecalibrator (Human)
- vcfs for GATK VariantRecalibrator (Mouse)
- EVA_SNP_all_mm10.vcf.gz
- MGP_SNP_indel_v5.vcf.gz (merged from MGP_SNP_v5.vcf.gz and MGP_indel_v5.vcf.gz)
- MGP_indel_v5.vcf.gz
- files used to filter out the background variants (Human)
- files used to filter out the background variants (Mouse)
git clone https://github.com/YangLab/BEIDOU.gitBEIDOU -f Function -1 Path_of_fastq1 -2 Path_of_fastq2 -o Output_path -n Output_name -c Path_of_config_file -t number_of_maximum_threads -g genome_build_version -d tmp_folder
[-f Function, "SNV", "Indel" or "all_steps"(default all_steps)]
[-1 Path of fastq1]
[-2 Path of fastq2]
[-o Output directory(default current directory)]
[-n Output name]
[-c Path of config file(default ./BEIDOU_config_GENOME_BUILD_VERSION)]
[-t Maximum_threads]
[-g Genome build version, "hg38" or "mm10"]
[-d wirtable temporary folder(default [Output directory]/BEIDOU_tmp)]- [Output directory]/[Output name]_Novel_SNVs and/or [Output directory]/[Output name]_Novel_Indels is the result of BEIDOU pipeline.
#[Software]
dir_of_bwa=~/bin
dir_of_samtools=~/bin
dir_of_gatk=~/bin
dir_of_picard=~/picard/build/libs
dir_of_bamtools=~/bin
dir_of_bcftools=~/bin
dir_of_lofreq=~/lofreq_star-2.1.3.1/bin
dir_of_Strelka2=~/strelka-2.9.10.centos6_x86_64/bin
dir_of_Scalpel=~/scalpel-0.5.4
dir_of_Manta=~/bin
dir_of_perl=~/bin
dir_of_parallel=~/bin
dir_of_intersectBed=~/bin
#[ref_genome]
ref_genome_path=path/to/hg38_all.fa
dict_of_ref_genome_path=path/to/hg38_all.dict
#[vcf_files_for_BaseRecalibrator]
dbsnp_vcf_for_BaseRecalibrator=path/to/NCBI_dbSNP_all_hg38.vcf.gz
#[vcf_files_for_VariantRecalibrator]
hapmap_vcf=path/to/hapmap_3.3.hg38.vcf.gz
file_1000G_omni_vcf=path/to/1000G_omni2.5.hg38.vcf.gz
file_1000G_phase1_vcf=path/to/1000G_phase1.snps.high_confidence.hg38.vcf.gz
dbsnp_vcf=path/to/dbsnp_146.hg38.vcf.gz
Mills_and_1000G_vcf=path/to/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
#[filtering file]
filtering_dbSNP_vcf=path/to/NCBI_dbSNP_all_hg38.vcf.gz
UCSC_RepeatMask_bed=path/to/UCSC_RepeatMask_hg38.bed
#[optional files(these files can be created automatic)]
dir_of_individual_chr_genome_range_bed=path/to/dir
dir_of_individual_chr_ref_genome_path=path/to/dirRunze Gao#, Zhi-Can Fu#, Xiangyang Li#, Ying Wang#, Jia Wei, Guangye Li, Lijie Wang, Jing Wu, Wei Xue, Xingxu Huang*, Li Yang*, Jia Chen*. Background levels of genome-wide off-target mutations induced by prime editor. 2020, xxxxxx
Copyright (C) 2020 YangLab. Licensed GPLv3 for open source use or contact YangLab (yanglab@picb.ac.cn) for commercial use.