Valid SNPIDs missing in vcf file

[matomol]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

latest

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

    nextflow run epi2me-labs/wf-human-variation \
    --out_dir ${VAR_DIR} \
    -w ${WORK_DIR} \
    --bam $ALN_DIR \
    --ref ${REFERENCE[$ARG1]} \
    --sample_name ${ARG0} \
    --bed $BED_REFERENCE/${REF_TYPE[$ARG1]}/hg38bed.bed \
    --bam_min_coverage 5 \
    --snp \
    --sv \
    --mod \
    --phased \
    --cnv \
    --str \
    -profile standard

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

I performed an analysis of the snp.vcf file and realized that although the variantes are correctly annotated the SNPID is missing. This is in particular true for SNPID with higher numbers, so that I assume that an outdated SNP reference database is used.

Relevant log output

Here are some examples:
Correctly annotated and the correct SNPID attached with the following SNPs
snpid   alleles     reference   alternatives
5930    (A, G)      A           (G,)
5927    (A, G)      A           (G,)

Correctly annotated but the proper SNPID missing are tzhe following variants
rs45508991,  rs72658861, rs11669576

Application activity log entry

There is nothing unusual. The output is of a normal basecalling.

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

no

[matomol]

Sorry a typo. Not basecalling but variant calling, of course.