glyma.Wm82.gnm2.div.Song_Hyten_2015.vcf

[jd-campbell]

I am trying to parse out 425 PIs from the glyma.Wm82.gnm2.div.Song_Hyten_2015.vcf using bcftools and have encountered an error:

[W::vcf_parse] Contig 'glyma.Wm82.gnm2.Gm01' is not defined in the header. (Quick workaround: index the file with tabix.)
Error: could not parse the input VCF

It looks like the header was not changed when the chromosome and contig names were changed.
header name:

##contig=<ID=Gm03,

Chromosome name:

glyma.Wm82.gnm2.Gm01

We need to review the vcf files that were changed and make sure the header is changed. Because if we do not change these headers these vcf files are almost useless.