VCF not valid

[bioinfo-chru-strasbourg]

VCF format specification (https://samtools.github.io/hts-specs/VCFv4.2.pdf) highly recommends (but not required) that the header include tags describing the contigs referred to in the VCF file. With samtools, output VCF of Scramble can not be view correctly due to contigs definition :

##contig=<ID=chr1>

Samtools command:

$ samtools view scramble.vcf
[main_samview] fail to read the header from "scramble.vcf"

Suggestion:
Add length and assembly as tags:

##contig=<ID=chr1,length=249250621,assembly=hg19>

[bioinfo-chru-strasbourg]

Another suggestion would be to add "FORMAT/GT" and a sample column, with heterozygous 0/1 by default