ValidateVariants gVCF mode error "covers a position previously traversed"

[bhanugandham]

User report:

ValidateVariants causes the error:

java -Xms32G -Xmx32G -jar /data/biosoftware/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar ValidateVariants -R ~/reference/reference.fasta -V $i -gvcf

And it causes the following error for all my files:

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A USER ERROR has occurred: In a GVCF all records must ordered. Record: [VC Unknown @ Super-Scaffold_2:1-4 Q. of type=SYMBOLIC alleles=[G*, <NON_REF>] attr={END=4} filters= covers a position previously traversed.

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This doesn't cause the error:

java -Xms32G -Xmx32G -jar /data/biosoftware/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar ValidateVariants -R ~/reference/reference.fasta -V $i

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/comment/59104#Comment_59104

[bhanugandham]

@ldgauthier and @jonn-smith

As discussed during the gatk office hours, this error traces back to ValidateVariants in GVCF mode being unable to handle variants with a lower start position than the previous contig.
Example:
Super-Scaffold_1 9238114 . T <NON_REF> . . END=9238123 GT:DP:GQ:MIN_DP:PL 0/0:12:0:11:0,0,0
Super-Scaffold_2 1 . G <NON_REF> . . END=4 GT:DP:GQ:MIN_DP:PL 0/0:31:93:31:0,93,1141