All outputs are based on the provided {OUTPUT_PREFIX} and an inferred {sample_name}.
The {sample_name} is extracted from the alignment file.
The name is taken from the first @RG tag in the alignment file header including a sample name.
{OUTPUT_PREFIX}.{sample_name}.vcf.gz- the primary VCF output containing copy number variant calls for the sample{OUTPUT_PREFIX}.{sample_name}.depth.bw- a bigwig depth track{OUTPUT_PREFIX}.{sample_name}.copynum.bedgraph- the copy number values calculated for each region
{OUTPUT_PREFIX}.log- the log file generated from running HiFiCNV{OUTPUT_PREFIX}.{sample_name}.maf.bw- a bigwig file containing the minor allele frequency measurements, only generated if a VCF file is provided
Additional outputs related to GC correction can be obtained with the --debug-gc-correction option, these are debug
outputs and may change in future updates:
{OUTPUT_PREFIX}.gc_frac.bw- A bigwig track of GC fraction windows (from the reference sequence) shared across all samples.{OUTPUT_PREFIX}.{sample_name}.gc_scaled_depth.bw- A bigwig depth track, similar to the standard bigwig depth output except that all depths are scaled by their region's GC correction factor. Note that the internal segmentation model uses GC correction factors directly instead of these adjusted depths, so these depths are only used for visualization.{OUTPUT_PREFIX}.{sample_name}.gc_correction_table.tsv- Sample GC correction factors as a function of GC fraction{OUTPUT_PREFIX}.{sample_name}.gc_reduction_factor.bw- A bigwig track of sample GC correction factors by region
HiFiCNV follows VCF format specification 4.2.
The QUAL field is reported as an average of the next-most-likely copy-number state for each bin from the HMM (see Methods).
It also includes a TARGET_SIZE filter flag for events that are smaller than 100kbp.
This filter can be disabled using the --disable-vcf-filters option.