├── .gitignore ├── LICENSE ├── README.md ├── images └── deep_variant_pipeline1.drawio.png ├── tools ├── fixSoftClippingOfBAM.r ├── fixSoftClippingOfBAM_multicore.r ├── flagCorrection.r ├── makeQnamesUnique.r ├── makeQnamesUnique_multicore.r └── removeRepeatedLowerQualSites.r └── variant_calling_code ├── illumina ├── 3_call_variants │ ├── 1_before_variant_calling │ │ └── manipulate_bam.sh │ ├── variantCalling_deepvariant.sh │ └── variantCalling_gatk.sh ├── 4_create_master_table │ └── createMasterTable_gatk_deepvariantButDv.Rmd └── 6_graphic_generation_and_method_comparisons │ └── create_all_illumin_plots_of_the_paper.Rmd ├── isoseq ├── 1_download_data │ ├── jurkat │ │ ├── dna_short_reads │ │ │ └── jurkat_dna_short_reads.sh │ │ └── iso_seq │ │ │ └── jurkat_iso_seq.sh │ ├── reference │ │ ├── genome.R │ │ ├── gtf.sh │ │ └── vcf.sh │ └── wtc11 │ │ ├── iso_seq │ │ └── wtc11_iso_seq.sh │ │ ├── not_filtered_ground_truth_vcf │ │ └── wtc11_vcf.sh │ │ └── rna_short_reads │ │ ├── ENCSR673UKZ.sh │ │ └── GSE175048.sh ├── 2_generate_ground_truth │ ├── jurkat │ │ └── generateGroundTruth_shortReads_gatk_jurkat.sh │ └── wtc11 │ │ └── groundTruth_wtc11_downloaded.sh ├── 3_call_variants │ ├── jurkat │ │ ├── 1_before_variant_calling │ │ │ └── align_flnc_reads_and_manipulate_bam.sh │ │ ├── 2_using_deepvariant │ │ │ └── variantCalling_deepVariant_isoSeq_jurkat.sh │ │ ├── 3_using_gatk │ │ │ └── variantCalling_gatk_isoSeq.sh │ │ ├── 4_using_clair3 │ │ │ └── variantCalling_clair3_isoSeq_jurkat.sh │ │ └── 5_using_nanocaller │ │ │ └── variantCalling_nanocaller_isoSeq_jurkat.sh │ └── wtc11 │ │ ├── 1_before_variant_calling │ │ └── align_flnc_reads_and_manipulate_bam.sh │ │ ├── 2_using_deepvariant │ │ └── variantCalling_deepVariant_isoSeq_wtc11.sh │ │ ├── 3_using_gatk │ │ └── variantCalling_gatk_isoSeq.sh │ │ ├── 4_using_clair3 │ │ └── variantCalling_clair3_isoSeq_wtc11.sh │ │ └── 5_using_nanocaller │ │ └── variantCalling_nanocaller_isoSeq_wtc11.sh ├── 4_create_master_table │ ├── jurkat │ │ └── mt_jurkat_allMethods_v7.Rmd │ └── wtc11 │ │ └── mt_wtc11_allMethods_v7.Rmd ├── 5_pre_analysis │ ├── 1_splice_junction_proximity_analysis │ │ └── splice_junction_proximity.R │ ├── 2_homopolymer_analysis │ │ └── identify_indels_within_and_outside_homopolimer_repeats.R │ └── 3_ase_analysis │ │ ├── 1_count_reads_per_allele.sh │ │ └── 2_identify_ase_snps.R └── 6_graphic_generation_and_method_comparisons │ └── create_all_plots_of_the_paper.Rmd └── nanopore ├── 3_call_variants ├── 1_before_variant_calling │ └── align_nanopore_reads_and_manipulate_bam.sh ├── variantCalling_clair3.sh ├── variantCalling_deepvariant.sh └── variantCalling_gatk.sh ├── 4_create_master_table └── createMasterTable_clair3_gatk_deepvariant.Rmd └── 6_graphic_generation_and_method_comparisons └── create_all_nanopore_plots_of_the_paper.Rmd /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vladimirsouza/lrRNAseqVariantCalling/HEAD/.gitignore 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