Error in process 'BAM_VARIANT_CALLING_TUMOR_ONLY_LOFREQ:MERGE_LOFREQ' unparsable vcf record with allele R

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Description of the bug

Gave the new tool lofreq a go with my tumour-only samples and all samples ran into this form of error in the MERGE_LOFREQ step:

htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 135144: unparsable vcf record with allele R, for input source: file:///fs04/scratch2/ar65/users/vajith/nxf_cache/sarek/35/780a82b18a734b5941bab6cb957587/SUPTG5.lofreq.chr1_122026460-124977944.vcf.gz

The record in question is the following:

chr1	248755122	.	R		881	PASS	DP=28;AF=0.000000;SB=2147483647;DP4=0,0,0,0

I looked at another file and got a similar case (in the exact same position too):

chr1	248755122	.	R		414	PASS	DP=33;AF=0.000000;SB=2147483647;DP4=0,0,0,0

Without too deep of a look it seems to be caused by the missing alt allele for these entries. I have attached all logs for the run, including the files in the process directory (excluding the vcfs but if necessary I can provide them too).

Command used and terminal output

nextflow -log /fs04/scratch2/ar65/workbench/sarek/2025-06-02_B022_nf-sarek/logs/.nextflow.log run nf-core/sarek -revision 3.5.1 -profile sarek,performance -config /projects/ar65/ngpmp_ref/projects/sarek_pipeline/nextflow.config -params-file /projects/ar65/ngpmp_ref/projects/sarek_pipeline/params.yml --input /fs04/scratch2/ar65/workbench/sarek/2025-06-02_B022_nf-sarek/inputs/samplesheet.csv --outdir /fs04/scratch2/ar65/workbench/sarek/2025-06-02_B022_nf-sarek/results --igenomes_base /fs04/scratch2/ar65/shared/references/genomes/igenomes --snpeff_cache /fs04/scratch2/ar65/shared/cache/snpeff --vep_cache /fs04/scratch2/ar65/shared/cache/vep -resume 055f806f-8481-4a01-872e-147b1b5711a1

Relevant files

sarek_lofreq_vcf_bug_logs.zip

System information

Nextflow version: 24.04.2
Hardware: HPC
Executor: slurm
Container engine: singularity
OS: Rocky Linux
Version of nf-core/sarek: 3.5.1