"chr" always added to chromosome names in combined_genotyped.vcf

[vladimirkovacevic]

Input BAM and reference genome are without "chr" while output combined_genotyped.vcf has "chr" in chromosome names. "chr" is added by script combine_combined.py:

# adds "chr"
if "chr" not in tab_split[0]:
    tab_split[0] = "chr" + tab_split[0]

Why?