When fed with vcf files from GATK4(version gatk-4.0.1.2) Mutect2, I got error message:
2018-04-26 12:37:19 - pcgr-validate-input - ERROR - According to the VCF specification, the VCF file (/workdir/input_vcf/AE188.mutect2.vcf.gz) is NOT valid:
ERROR: Line 119: Format is not a colon-separated list of alphanumeric strings
However the lines before line 119 are all the same as line 119
The FORMAT in Mutect2 vcf in line 119 looks the following,
GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB
AE188.mutect2.vcf.gz
Is that the underscore that is not accepted?
When fed with vcf files from GATK4(version gatk-4.0.1.2) Mutect2, I got error message:
2018-04-26 12:37:19 - pcgr-validate-input - ERROR - According to the VCF specification, the VCF file (/workdir/input_vcf/AE188.mutect2.vcf.gz) is NOT valid:
ERROR: Line 119: Format is not a colon-separated list of alphanumeric strings
However the lines before line 119 are all the same as line 119
The FORMAT in Mutect2 vcf in line 119 looks the following,
GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB
AE188.mutect2.vcf.gz
Is that the underscore that is not accepted?