Unable to write MatrixTable (VCFParseError)

Hail Query & hailctl
1

Hi all, I am importing a large joint-called VCF, and when I try to write it to a MatrixTable, I received this error:
Error summary: VCFParseError: error while parsing info field 'dbSNP151__COMMON': invalid character ',' in integer literal
May I know if there is an argument to get around this, or do I need to fix the VCF? Thank you very much!

2

The VCF probably has an incorrect NUMBER in the INFO header line for that field. My guess is that is says the number is 1 but it really needs to be one of the array designators (A/R/G/./2/etc).

3

Thank you for your response. Can I ask if there is there a way to rectify this in Hail?

4

You can get around this by creating a fixed header as a separate file, and using the header_file argument to import_vcf.