Running with --split false only writes first contig header

[dennishendriksen]

Running

java -jar vcf-tools-0.1.jar vcf-generator --in <input> --ref human_g1k_v37_phiX.fasta --out <output> --split false

writes a VCF with header

##fileformat=VCFv4.2
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>

with variants in multiple chromosomes. The contig headers for other chromosomes are missing.

Using the VCF with bcftools results in:

[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
Encountered an error, cannot proceed. Please check the error output above.