RADAR/RADAR.conf at master · YangLab/RADAR · GitHub

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#### genomic sequence index for aligner
## genome build version
## Example: genome_build_version=hg38
genome_build_version=

## Ribosomal DNA (rDNA) sequence index for BWA MEM, which can be created by command "bwa index ~/reference/Human/RNA_45S5/RNA45S5.fa"
## Example: rDNA_index_bwa_mem=~/reference/Human/RNA_45S5/RNA45S5.fa
rDNA_index_bwa_mem=

## Path to reference genome
## Example: genome_fasta=~/reference/Human/hg38/hg38_all.fa
genome_fasta=

## Reference genome sequence index for HISAT2, which can be created by command "hisat2-build ~/reference/Human/hg38/hg38_all.fa ~/reference/Human/hg38/hg38_all.fa"
## Example: genome_index_hisat2=~/reference/Human/hg38/hg38_all.fa
genome_index_hisat2=

## Reference genome sequence index for BWA MEM, which can be created by command "bwa index ~/reference/Human/hg38/hg38_all.fa"
## Example: genome_index_bwa_mem=~/reference/Human/hg38/hg38_all.fa
genome_index_bwa_mem=

## Reference genome sequence index for Blat, which can be created by command "tools/faToTwoBit ~/reference/Human/hg38/hg38_all.fa ~/reference/Human/hg38/hg38_all.fa.2bit"
## Example: genome_index_blat=~/reference/Human/hg38/hg38_all.fa.2bit
genome_index_blat=

## Reference genome sequence dictionary for GATK in the directory of reference genome, which can be created by command "gatk CreateSequenceDictionary -R ~/reference/Human/hg38/hg38_all.fa"
## Example: genome_index_gatk=~/reference/Human/hg38/hg38_all.dict
genome_index_gatk=


#### Variants annotation: dbSNP, 1000Genome, EVS
## Total variants annotation from NCBI dbSNP (http://www.ncbi.nlm.nih.gov/SNP/)
## Example of the total .vcf file: dbSNP_all=~/annotation/Human/hg38/SNP/dbSNP_b151/NCBI_dbSNP_b151_all_hg38.vcf
## Example of the GATK index for total .vcf: dbSNP_all_index_gatk=~/annotation/Human/hg38/SNP/dbSNP_b151/NCBI_dbSNP_b151_all_hg38.vcf.idx, which can be created by command "gatk IndexFeatureFile -F ~/annotation/Human/hg38/SNP/dbSNP_b151/NCBI_dbSNP_b151_all_hg38.vcf"
dbSNP_all=
dbSNP_all_index_gatk=

## SNP annotation from NCBI dbSNP divided by chromosome (http://www.ncbi.nlm.nih.gov/SNP/)
## Example of the folder for NCBI dbSNP divided by chromosome: SNP_dbSNP_divided_by_chromosome=~/annotation/Human/hg38/SNP/dbSNP_b151/split_chr
SNP_dbSNP_divided_by_chromosome=

## SNP annotation from The 1000 Genomes Project (https://www.internationalgenome.org/) divided by chromosome
## Example of the folder for SNP divided by chromosome: SNP_1000Genome_divided_by_chromosome=~/annotation/Human/hg38/SNP/1000genomes/split_chr
SNP_1000Genome_divided_by_chromosome=

## SNP annotation from The University of Washington Exome Sequencing Project (http://evs.gs.washington.edu/EVS/) divided by chromosome
## Example of the folder for SNP divided by chromosome: SNP_EVS_divided_by_chromosome=~/annotation/Human/hg38/SNP/EVS/split_chr
SNP_EVS_divided_by_chromosome=

#### Genome annotation
## Annotation of Alu, repetitive non-Alu, non-repetitive genomic region in the BED format
## Example of Alu annotation: annotation_Alu=~/annotation/Human/hg38/Alu.bed
## Example of repetitive non-Alu annotation: annotation_Repetitive_non_Alu=~/annotation/Human/hg38/Repetitive_non-Alu.bed
## Example of all repetitive annotation: annotation_All_repetitive=~/annotation/Human/hg38/All_repetitive.bed
annotation_Alu=
annotation_Repetitive_non_Alu=
annotation_All_repetitive=

## Annotation of RepeatMasker simple repeats from UCSC in BED format
## Example: annotation_RepeatMasker_simple_repeats=~/annotation/Human/hg38/UCSC_RepeatMask_SimpleRepeats_hg38.bed
annotation_RepeatMasker_simple_repeats=

## Annotation of known splice sites in BED format, which is used as the input of option "--known-splicesite-infile" during HISAT2 mapping. Official website of HISAT2 (https://ccb.jhu.edu/software/hisat2/index.shtml) has detailed how to create it.
### Example: annotation_splice_sites=~/annotation/Human/hg38/ref_all_spsites_hg38.bed
annotation_splice_sites=

## Annotation of intronic 4 bp flanking splice sites
## Example: annotation_intronic_4site=~/annotation/Human/hg38/hg38_intronic_4site.bed
annotation_intronic_4site=

## Annotation of transcribed strands of genes
## Example: annotation_gene_transcribed_strands=~/annotation/Human/hg38/ref_UCSC_refFlat.bed
annotation_gene_transcribed_strands=