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rkimoakbioinformatics / oakvar

Genomic variant analysis platform
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feature request: autodetect option for reference genome #18

Closed antonkulaga closed 1 year ago

antonkulaga commented 2 years ago

Right now users have to select the refernce genome themselves and sometimes they make mistakes. At the same time usually reference genome is mentioned in the VCF file itself, maybe on top of hg37/38 you can provide detect_from_file option for reference genome>

rkimoakbioinformatics commented 2 years ago

@antonkulaga Please check with the new release oakvar 2.5.39. For VCF files, vcf-converter 2.1.8 should be used. One change is that now you can use input files of different genome assemblies. The genome assembly of each VCF-format input file is examined. -l option as in ov run -l hg19 will override any auto-detected genome assembly.

antonkulaga commented 1 year ago

I think it is already implemented