the vcf file from haplotypecaller was not annotated by snpeff and vep

[ybdong919]

Description of the bug

After I got snp vcf files from strelka, freebayes, mpileup, and haplotypecaller, I tried to annotate them by snpeff and vep. Finally, the vcf file from haplotypecaller was not annotated by snpeff and vep, but other vcf files from strelka, freebayes and mpileup are all successfully annotated by snpeff and vep.
Do you know why?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[FriederikeHanssen]

Can you please share the command you used & the version of sarek you ran?

[ybdong919]

1. Params.yaml:

input: './samplesheet.csv'
outdir: './results/'
#genome: 'null'
tools: 'mpileup,haplotypecaller,freebayes,strelka,snpeff,vep'
skip_tools: 'baserecalibrator,baserecalibrator_report,dnascope_filter'
#step: 'annotate'
igenomes_ignore: 'true'
snpeff_cache: '//snpeff_cache'
snpeff_db: 'MN908947.3'
vep_cache: '//vep_cache'
vep_species: 'sars_cov_2'
vep_genome: 'ASM985889v3'
vep_cache_version: '101'

fasta: '//nCoV-2019.reference.fasta'
fasta_fai: '//nCoV-2019.reference.fasta.fai'
only_paired_variant_calling: 'true'

2. The running command is:
   $nextflow run ./sarek/main.nf -profile singularity -params-file params.yaml

3. sarek version is :
   https://github.com/asp8200/sarek/tree/modify_snpeff_cache_setup