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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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GATK LiftoverVcf not recognized vcf4.2 file created by plink1.9 #7460

Open Xiao-lin-Liu opened 3 years ago

Xiao-lin-Liu commented 3 years ago

Hello, I was using GATK4 LiftoverVcf to adjust the coordinates of variants in my vcf4.2 file (created by plink1.9) to hg38 reference build. However, I got this error: The provided VCF file is malformed at approximately line number 218: Insertions/Deletions are not supported when reading 3.x VCF's. Please convert your file to VCF4 using VCFTools, available at http://vcftools.sourceforge.net/index.html

And I tried to use vcf-convert in vcftools to convert my vcf4.2 file to vcf4.0 form, but the problem was not solved.

droazen commented 3 years ago

@Sasakawamiwa Can you check whether any of the alleles at line 218 contain IUPAC bases? In particular, is there a D present? If you could share this entire line with us (without the genotypes) that would be helpful.