chromosome name

[sotaro-kanematsu]

I am using facets to uncover allele-specific somatic copy number alternations using clinical tumor-normal pairs.
I run the cnv_facets.R script as below.

cnv_facets.R --gbuild hg19 -t Tumor.bam -n Normal.bam -vcf common_all_20170710.vcf.gz -o Nomal_Tumor_cnv_facets_output

I used hs37d5a.fa as a reference sequence in mapping, and so my bam files do not have prefixes (e.g. 1, 2, 3.....Y) as well as the common SNP vcf file.
On the other hand, hg19 has prefixes (e.g. chr1, chr2...chrY), so If I run the above script, an error occurs. (I know the script work well if I change the header of bam files and add "chr" prefix to vcf file, however I thought it is supposed inefficient to fix bam files or change the reference.
How should I fix the cnv_facets.R script?

[veseshan]

Since cnv_facets is at https://github.com/dariober/cnv_facets have you asked @dariober