Output files for the virus variant caller pipeline on the full 4sU-seq data set for HSV-1 mutant strains

results.zip: zip-archive containing the full workflow results for the 4sU-seq data. This contains the following directories: bcftools: directory containing output files from bcftools in the variant call format (VCF). varscan: directory containing output files from VarScan in a (comparable) variant call format (VCF). consistent: directory containing files with consistent SNPs for each sample (tab-separated file, columns: CHR=chromosome, POS=chromosome position (1-based), REF=nucleotide in reference genome, ALT=observed nucleotide) strains: directory containing files with virus strain predictions for each sample, including distances for all strains. gtfMatcher_SNPs: directory containing files with information about features (e.g. genes) that matched to consistent SNPs. genomeCoverage: directory containing bedgraph files of read coverage per position. clippedReads: directory containing BAM files with only clipped reads. deletions: directory containing files with detected deletions (tab-separated file, columns: CHR=chromosome, START=start of deletion, END=end of deletion, positions are 1-based and inclusive). insertions: directory containing files with detected insertions (tab-separated file, columns: CHR=chromosome, POSITION=genomic position of insertion (1-based), OVERLAP=overlap between the ends of the inserted sequence and the surrounding genome sequences). consensus: directory containing fasta files with consensus sequences of insertion start and end extracted from clipped reads. gtfMatcher_deletions: directory containing files with information about features (e.g. genes) that matched to detected deletions. gtfMatcher_insertions: directory containing files with information about features (e.g. genes) that matched to detected insertions. SPades: directory containing output directories for the assemblies by SPades. bwaMEM: directory containing SAM files that store information about the alignment of consensus sequences to the assembly. assemblyAnalyzer: directory containing fasta files with extracted insertion sequences. blast_results.zip: Blast results for the extracted insertion sequences (from assemblyAnalyzer directory)