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

dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Apache License 2.0

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"chr" always added to chromosome names in combined_genotyped.vcf #67

Open vladimirkovacevic opened 5 years ago

vladimirkovacevic commented 5 years ago

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?