There are some errors of RADAR.conf #1
Description
Hi Prof. Yang,
I’m Jian-Guo, works as PhD student in Universitätsklinikum Erlangen.
Thanks for your RADAR tool, now I have some questions of this document.
There are some errors of RADAR.conf
#### genomic sequence index for aligner
## genome build version
## Example: genome_build_version=hg38
genome_build_version=hg38
## 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=
(I didn’t find this .fa)
## Path to reference genome
## Example: genome_fasta=~/reference/Human/hg38/hg38_all.fa
genome_fasta=~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa
## Reference genome sequence index for HISAT2, which can be created by command "hisat2-build ~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa ~/hdd/reference/hg38_ek12/hisat2”
## Example: genome_index_hisat2=~/reference/Human/hg38/hg38_all.fa
genome_index_hisat2=~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa
The HISAT2 index command is : hisat2-build --ss hg19.splice_sites.gtf --exon hg19.exons.gtf genome/hg19/hg19.fa hg19, so this command need gtf and fa. But your command only fa.
## Reference genome sequence index for BWA MEM, which can be created by command "bwa index ~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa"
## Example: genome_index_bwa_mem=~/reference/Human/hg38/hg38_all.fa
genome_index_bwa_mem=~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa
## 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"
#~/biosoft/RADAR/tools/faToTwoBit ~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa ~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa.2bit
## Example: genome_index_blat=~/reference/Human/hg38/hg38_all.fa.2bit
genome_index_blat=~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa.2bit
## Reference genome sequence dictionary for GATK in the directory of reference genome, which can be created by command "~/biosoft/gatk-4.1.8.1/gatk CreateSequenceDictionary -R ~/hdd/reference/hg38_ek12/GRCh38.p13.genome.fa"
## Example: genome_index_gatk=~/reference/Human/hg38/hg38_all.dict
genome_index_gatk=~/hdd/reference/hg38_ek12/GRCh38.p13.genome.dict
#### 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=
I didn’t find this, please help me.
## 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=
I didn’t find this, please help me.
## 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=
I didn’t find this, please help me.
## 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=
I didn’t find this, please help me.
#### 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=
I didn’t find this, please help me.
## 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=
I didn’t find this, please help me.
## 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=
Could you please point to point response my request.
Best,