The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth information, variants and DNA Gene features
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Reference sequence is assumed to be available from NCBI if not found in input directory #54
When parsing depths from a BAM file, the reference sequence ID is retrieved from the BAM header info, however, that reference sequence may not always be an NCBI sequence. This is an issue with IRMA output where BAM files have reference sequence IDs that are fairly generic (e.g. "A_PB2"). In this case, it may be preferable to not try to retrieve any ref seq and omit it entirely from the output or spoof it based on a consensus sequence.
When parsing depths from a BAM file, the reference sequence ID is retrieved from the BAM header info, however, that reference sequence may not always be an NCBI sequence. This is an issue with IRMA output where BAM files have reference sequence IDs that are fairly generic (e.g. "A_PB2"). In this case, it may be preferable to not try to retrieve any ref seq and omit it entirely from the output or spoof it based on a consensus sequence.