Releases · MelbourneGenomics/cpipe

Gene list input instead of bed files

The process for specifying target regions has changed. Instead of specifying bed files, genes are specified, which are then converted to regions based on the exon.bed file.
The user guide explains in more detail.

The QC report is now generated as HTML instead of PDF. It also includes new fields and documentation.

The existing Excel gap report has been superseded by CSV based gap reports with additional annotation (see Cpipe Outputs)
*Although the Excel gap report is still present in this version we expect to replace it with individual annotated gap reports in future releases.

INTERVAL_PADDING_CALL: this value is the overall padding added to each exon when calling any type of variant.
INTERVAL_PADDING_SNV: this value is the overall padding added to each exon when calling SNPs.
INTERVAL_PADDING_INDEL: this value is the overall padding added to each exon when calling indels.
ALLOW_SYNONYMOUS_INTRON: normally, synonymous variants are given priority 0, however, if the variant is synonymous and within this many bases of an exon boundary on the intronic side, it will not be filtered.
ALLOW_SYNONYMOUS_EXON: normally, synonymous variants are given priority 0, however, if the variant is synonymous and within this many bases of an exon boundary on the exonic side, it will not be filtered.