BEIDOU_config_demo_mm10

#[Software]
dir_of_bwa=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_samtools=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_gatk=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_picard=/picb/rnomics3/xuew/software/WGS/picard/build/libs
dir_of_bamtools=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_bcftools=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_lofreq=/picb/rnomics3/xuew/software/WGS/lofreq_star-2.1.3.1/bin
dir_of_Strelka2=/picb/rnomics3/xuew/software/WGS/strelka-2.9.10.centos6_x86_64/bin
dir_of_Scalpel=/picb/rnomics3/xuew/software/WGS/scalpel-0.5.4
dir_of_Manta=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_perl=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_parallel=/picb/rnomics3/xuew/software/anaconda2019/bin
dir_of_intersectBed=/picb/rnomics3/xuew/software/anaconda2019/bin
#[ref_genome]
ref_genome_path=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/mapping_tools_index/mm10_all.fa
dict_of_ref_genome_path=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/mapping_tools_index/mm10_all.dict
#[vcf_files_for_BaseRecalibrator]
dbsnp_vcf_for_BaseRecalibrator=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/NCBI_dbSNP_all_mm10.vcf
#[vcf_files_for_VariantRecalibrator]
dbsnp_vcf=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/NCBI_dbSNP_all_mm10.vcf #NCBI_dbSNP_b142_all_mm10.vcf.gz #Due NCBI stopped support for all non-human organisms in dbSNP, in 2017. The dbSNP file was from EVA no dbSNP release version, see the readme in the same dir for further info.  #NCBI_dbSNP_b142_all_mm10.vcf.gz
MGP_vcf=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/MGP_SNP_indel_v5.vcf.gz 
MGP_indel_vcf=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/MGP_indel_v5.vcf.gz #/picb/rnomics3/xuew/Human/backup/GATK_bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
#[filtering file]
filtering_dbSNP_vcf=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/NCBI_dbSNP_all_mm10.vcf
UCSC_RepeatMask_bed=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/UCSC_RepeatMask_mm10.bed
#[optional files(these files can be created automaticcally)]
#dir_of_individual_chr_genome_range_bed=/picb/rnomics3/xuew/Human/backup/hg38_common
dir_of_individual_chr_ref_genome_path=/picb/rnomics4/rotation/fuzhican/project/ABE_transcriptomics_off_target/dep_files/mm10/Genome_per_chrom