filename,description
extra_files-dat_ase_analysis.rds,Data to make the plot for the ASE analysis.
extra_files-dat_homopolymer_analysis.rds,Data to make the plot for the homopolymer analysis.
extra_files-indel_splice_junction_proximity_analysis.rds,Data to make the plot for the indel proximity to splice junctions analysis.
extra_files-master_tables-mt_jurkat_allMethods_filtered_v7.rds,The filtered master table generated and used to study the Jurkat dataset.
extra_files-master_tables-mt_jurkat_allMethods_notFiltered_v7.rds,The full master table generated and used to study the Jurkat dataset.
extra_files-master_tables-mt_wtc11_allMethods_filtered_v7.rds,The filtered master table generated and used to study the WTC-11 dataset.
extra_files-master_tables-mt_wtc11_allMethods_notFiltered_v7.rds,The full master table generated and used to study the WTC-11 dataset.
extra_files-snp_splice_junction_proximity_analysis.rds,Data to make the plot for the SNP proximity to splice junctions analysis.
jurkat-data_manipulation-aln_s.bam,Iso-Seq reads (Jurkat) aligned to the reference genome; sorted bam.
jurkat-ground_truth-jurkat_merged.recal_pass.vcf.gz,Variants called from short reads (Jurkat); the diploid ground truth for Jurkat cells.
jurkat-variant_calling_from_isoseq-clair3-c3-pileup_pass.vcf.gz,Variants called (Jurkat) by Clair3 when input BAM not manipulated.
jurkat-variant_calling_from_isoseq-clair3-c3_sncr-pileup_pass.vcf.gz,Variants called (Jurkat) by Clair3 when input BAM manipulated by SplitNCigarReads.
jurkat-variant_calling_from_isoseq-clair3-c3_sncr_fc-pileup_pass.vcf.gz,Variants called (Jurkat) by Clair3 when input BAM manipulated by SplitNCigarReads and flagCorrection.
jurkat-variant_calling_from_isoseq-clair3-mix-pileup_pass_mix_norep.recode.vcf.gz,"Variants called (Jurkat) by Clair3; SNPs called from BAM not manipulated, and indels called from BAM manipulated by SplitNCigarReads and flagCorrection."
jurkat-variant_calling_from_isoseq-deepvariant-dv-deepvariant_calls_pass.vcf.gz,Variants called (Jurkat) by DeepVariant when input BAM not manipulated.
jurkat-variant_calling_from_isoseq-deepvariant-dv_sncr-deepvariant_calls_pass.vcf.gz,Variants called (Jurkat) by DeepVariant when input BAM manipulated by SplitNCigarReads.
jurkat-variant_calling_from_isoseq-deepvariant-dv_sncr_fc-deepvariant_calls_pass.vcf.gz,Variants called (Jurkat) by DeepVariant when input BAM manipulated by SplitNCigarReads and flagCorrection.
jurkat-variant_calling_from_isoseq-gatk-isoSeq_jurkat.recal_pass.vcf.gz,Variants called (Jurkat) by standard GATK pipeline; called from BAM manipulated by SplitNCigarReads.
jurkat-variant_calling_from_isoseq-nanocaller-nc_sncr-variant_calls.final.vcf.gz,Variants called (Jurkat) by NanoCaller when input BAM manipulated by SplitNCigarReads.
wtc11-ase_analysis-ase_read_count_tables-ase_read_count_all.table,"A text-like file that stores a table generated by GATK’s ASEReadCounter function, with read counts per allele (WTC-11)."
wtc11-data_manipulation-aln_s.bam,Iso-Seq reads (WTC-11) aligned to the reference genome; sorted bam.
wtc11-variant_calling_from_isoseq-clair3-c3-pileup_pass.vcf.gz,Variants called (WTC-11) by Clair3 when input BAM not manipulated.
wtc11-variant_calling_from_isoseq-clair3-c3_sncr-pileup_pass.vcf.gz,Variants called (WTC-11) by Clair3 when input BAM manipulated by SplitNCigarReads.
wtc11-variant_calling_from_isoseq-clair3-c3_sncr_fc-pileup_pass.vcf.gz,Variants called (WTC-11) by Clair3 when input BAM manipulated by SplitNCigarReads and flagCorrection.
wtc11-variant_calling_from_isoseq-clair3-mix-pileup_pass_mix_norep.recode.vcf.gz,"Variants called (WTC-11) by Clair3; SNPs called from BAM not manipulated, and indels called from BAM manipulated by SplitNCigarReads and flagCorrection."
wtc11-variant_calling_from_isoseq-deepvariant-dv-deepvariant_calls_pass.vcf.gz,Variants called (WTC-11) by DeepVariant when input BAM not manipulated.
wtc11-variant_calling_from_isoseq-deepvariant-dv_sncr-deepvariant_calls_pass.vcf.gz,Variants called (WTC-11) by DeepVariant when input BAM manipulated by SplitNCigarReads.
wtc11-variant_calling_from_isoseq-deepvariant-dv_sncr_fc-deepvariant_calls_pass.vcf.gz,Variants called (WTC-11) by DeepVariant when input BAM manipulated by SplitNCigarReads and flagCorrection.
wtc11-variant_calling_from_isoseq-gatk-isoSeq_wtc11.recal_pass.vcf.gz,Variants called (WTC-11) by standard GATK pipeline; called from BAM manipulated by SplitNCigarReads.
wtc11-variant_calling_from_isoseq-nanocaller-nc_sncr-variant_calls.final.vcf.gz,Variants called (WTC-11) by NanoCaller when input BAM manipulated by SplitNCigarReads.