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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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v c f #22

Closed xiucz closed 4 years ago

xiucz commented 4 years ago

Hi, @dariober In the R package or the old verisons, there seemed no -vcf parameter in the command line. I also could not find any in the paper. Can you give comments on this parameter? What does it mean or use for?

Thank you. Xiucz

dariober commented 4 years ago

Hi Xiucz - The --vcf option specifies a VCF file of known SNPs to be used as markers to detect allele copy number changes. This file is passed to the program snp-pileup whose output goes into the functions of the original FACETS package. So the original facets package doesn't mention a VCF file because its input is already a pileup file. This should be explained in the README of cnv_facets and in the vignettes of facets.

Hope this helps Dario