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1 changed files with 10 additions and 9 deletions
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@ -16,21 +16,22 @@ Specific configurations for `MUNIN` has been made for rnavar.
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Genome references
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`fasta` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa`
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`fasta_fai` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai`
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`gtf` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf`
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`gene_bed` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed`
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* Path to `fasta`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa`
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* Path to `fasta_fai`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai`
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* Path to `gtf`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf`
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* Path to `gene_bed`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed`
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Known genome resources
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`dbsnp set to` `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz`
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`dbsnp_tbi set` to `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi`
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`known_indels set` to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz`
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`known_indels_tbi` set to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi`
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* Path to `dbsnp`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz`
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* Path to `dbsnp_tbi`: `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi`
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* Path to `known_indels`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz`
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* Path to `known_indels_tbi`: `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi`
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STAR index
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`star_index` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/star150bp.idx/`
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* Path to `star_index`: `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/STAR.2.7.9a_2x151bp/`
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* Params `read_length` set to `151`
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Variant annotation configurations
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