Unable to parse header in IGV


Possible cause

Recommended action

The following error is seen when you attempt to view one of the variants in Integrative Genomics Viewer (IGV):
Unable to parse header:
Your input file has a malformed header: unknown column name 'CHR'; it does not match a legal column header name.

IGV does not load variants and displays this error message when a VCF file uses CHR instead of CHROM for a column header name.

To avoid this error, use the CHROM column header name in input VCF files. For example, #CHROM POS ID REF.