population_vcfs not working

[Larrycpan]

I'm using custom reference for variant calling (v1.10), and set the parameter --population_vcfs="/path/to/my/reference.vcf.gz". But it ran to an error and told me that there is no population_vcfs parameter. I also tried --make_examples_extra_args="population_vcfs=/path/to/my/reference.vcf.gz" , it didn't working yet, and seems using the default hg38 PON. If this paramter cannot be successfully set up, can I ignore the warning and keep the job running, and I manually filter out the germline variants from the output vcf using my germline reference? Look forward your reply!

[kishwarshafin]

@Larrycpan the parameter is --pon_filtering so you provide a VCF instead of the default VCFs and it will use that for filtering. Use it with run_deepsomatic binary.

[Larrycpan]

@Larrycpan the parameter is --pon_filtering so you provide a VCF instead of the default VCFs and it will use that for filtering. Use it with run_deepsomatic binary.

Thanks for your reply. I switched to the --pon_filtering, but not working, encountering the same warning. I double checked the contig name of reference fasta, pon vcf.gz and bam files, and the names are all consistent. If not working, can I ignore this warning and filtering them manually in the end?

Here's my code

/share/app/singularity/3.8.1/bin/singularity exec ${NV_FLAG} \
    -B "${SINGULARITY_BIND}" \
    "/share/App/deepsomatic_1.10.sif" \
    run_deepsomatic \
    --model_type="WGS_TUMOR_ONLY" \
    --ref="/input/tom/reference/fasta/test.corrected.fa" \
    --reads_tumor="/input/tom/Project/test.dedup.bam" \
    --pon_filtering="/input/tom/reference/custome.pon.vcf.gz" \
    --output_vcf="/output/test.vcf.gz" \
    --output_gvcf="/output/test.g.vcf.gz" \
    --sample_name_tumor="test_tumor" \
    --num_shards="16" \
    --logging_dir="/output/logs/test" \
    --intermediate_results_dir="/output/tmp/test" \
    --use_default_pon_filtering=false \
    --dry_run=false

[pichuan]

Hi @Larrycpan , can you tell us more about what error you're seeing?

Your original message mentioned: "it ran to an error and told me that there is no population_vcfs parameter".

After you switched to --pon_filtering, I would think that the error message you're getting would be different. Can you paste the error message you have now?