All outputs are based on the provided {OUTPUT_PREFIX} and a 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 file containing the depth measurements{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
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.