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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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pytorDG=0 for everything when using pytorCL=combined_mosaic #189

Closed trjojack closed 10 months ago

trjojack commented 1 year ago

When using the combined caller (combined_mosaic), all entries in the vcf file have pytorDG=0 which prevents filtering out calls close to gaps in the ref genome, as for the rd_mean_shift caller.

arpanda commented 1 year ago

Currently, the combined caller (combined_mosaic) output doesn't have DG value, it has pNS [fraction of reference genome gaps (Ns) within call segments]. Please have a look at this description.

The VCF input doesn't report the pNS value, I will update the vcf output to include the pNS field.

Thank you, Arijit