Issue with vt normalize and indels

[ESDeutekom]

I have the same issue as here (few years later). The command vt validate throws the name core dump error. I tried removing the .fai file, vt made a new one, but it gave me the same error. Only when the del AATG/A is reached. VCF files created by gatk, deepvariant and freebayes.

Also tried -w 0.

output:

normalize v0.5

options: input VCF file dv_filtered_decomp.vcf
[o] output VCF file dv_filtered_decomp_norm.vcf
[w] sorting window size 10000
[n] no fail on reference inconsistency for non SNPs false
[q] quiet false
[d] debug true
[r] reference FASTA file /mnt/db/reference_genomes/homo_sapiens/DRAGEN/Homo_sapiens_assembly38_masked.fasta

chr1:13684:C/T
chr1:13813:T/G
chr1:13838:C/T
chr1:14653:C/T
chr1:14907:A/G
chr1:14930:A/G
chr1:15118:A/G
chr1:15211:T/G
chr1:16378:T/C
chr1:16495:G/C
chr1:16949:A/C
chr1:17385:G/A
chr1:17407:G/A
chr1:30548:T/G
chr1:30923:G/T
chr1:109488:G/A
chr1:124855:A/G
chr1:129010:AATG/A
/.lsbatch/1739805563.4255437: line 8: 2866095 Floating point exception (core dumped) vt normalize -d -r Homo_sapiens_assembly38_masked.fasta -o dv_filtered_decomp_norm.vcf dv_filtered_decomp.vcf

Kind regards,