Closed xiucz closed 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
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