Expects format column in all VCFs

[danhalligan]

According to VCF specification the "FORMAT" column is not mandatory:
http://samtools.github.io/hts-specs/VCFv4.2.pdf
This script fails due to line 219, that always expects a format column.

[zhanxw]

Thanks for reporting. But the specification section 1.4.2 mentions the FORMAT column should be present in the genotype fields. FORMAT can only be omitted in the header part. So I think line 219 should be kept as it is now.

[danhalligan]

I believe that if there are genotype fields present, then you must have a format column, but I think still think it is possible to have valid VCF files with no genotype columns and no format column, though admittedly this situation might be rare. As an example though, I think the vcf files containing dbSNP variants lack a format column: http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/#all-00