how to convert vcf4.2 to vcf4.1? - Githubissues

francois-a / fastqtl

Enhanced version of the FastQTL QTL mapper

GNU General Public License v3.0

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how to convert vcf4.2 to vcf4.1? #30

Closed jingydz closed 10 months ago

jingydz commented 11 months ago

$ /xxx/software/fastqtl/python/run_FastQTL_threaded.py --help positional arguments: vcf Genotypes in VCF 4.1 format bed Phenotypes in UCSC BED extended format prefix Prefix for output file name

Hi, I find my vcf file format is ##fileformat=VCFv4.2, but the fastQTL need the vcf4.1. How can I convert the vcf4.2 to vcf4.1?

Thanks in advance.

francois-a commented 10 months ago

There should be no need to convert from 4.2 to 4.1. Please consider using tensorQTL instead.