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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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vcf file #32

Closed sotaro-kanematsu closed 3 years ago

sotaro-kanematsu commented 3 years ago

Hi I would like to ask the genome version of output vcf file via cnv_facets.R (maybe named *.vcf). I used snp vcf file named common_all_20170710.vcf.gz (hg19) as input, however, when I check the output vcf file, the reference version was hg38. Does cnv_facets convert genome version automatically? or I do wrong something ?

dariober commented 3 years ago

Hi- The genome version in the vcf header is taken from the command line argument --gbuild/-g where the default is hg38. If you are working with hg19, you should use cnv_facets.R --gbuild hg19 ...

Does it make sense? If not can you post the command line you used and perhaps the header of the VCF output?