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Run PVT to detect structural variants (fusions, read-throughs, ITDs, PTDs, InDels)
find_sv.py --gbam <contigs_to_genome_bam> --tbam <contigs_to_transcripts_bam> --transcripts_fasta <indexed_transcripts_fasta> --genome_index <GMAP index genome directory and name> --r2c <reads_to_contigs_bam> <contigs_fasta> <gtf> <genome_fasta> <outdir> -
Run PVT to detect novel splice variants (exon_skipping, novel_exon, novel_intron, novel_donor, novel_acceptor, retained_intron)
map_splice.py <contigs_to_genome_bam> <contigs_fasta> <gtf> <genome_fasta> <outdir> --r2c <reads_to_contigs_bam> --suppl_annot <supplmental_annotations> -
Run full (assembly + analysis) TAP in targeted mode
tap.py <sample> <outdir> --bf <target_genes.bf> --fq_list <file_listing_FASTQ_pairs> --k <space-delimited k values> --readlen <read_length> --nprocs <number_of_processes> --params <parameters_file> -
Run full (assembly + analysis) TAP for entire transcriptome
tap.py <sample> <outdir> --fq_list <file_listing_FASTQ_pairs> --k <space-delimited k values> --readlen <read_length> --nprocs <number_of_processes> --params <parameters_file> -
Run TAP for just de novo assembly
tap.py <sample> <outdir> --fq_list <file_listing_FASTQ_pairs> --k <space-delimited k values> --readlen <read_length> --nprocs <number_of_processes> --only_assembly