query region doesn't contain variants

[alisamatisse]

Hello,

Hope you can help me!
I called variants with deepvariant v1.8.0 for my region of interest, and then I wanted to bnchmark them with hap.py

<...>
# Define the reference and benchmark files
REFERENCE="hg38_MHC.fa"
BENCHMARK_BED="HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed"
OUTPUT_DIR="happy_trios"
ENGINE="vcfeval"
PASS_ONLY="--pass-only"
REGION="chr1:151857524-153780694"

export APPTAINER_CACHEDIR=<...>
export APPTAINER_TMPDIR=<...>
export HGREF=<...>

mkdir -p "${OUTPUT_DIR}"

for VCF in deepvariant_output/hifi_trio_hg38/*.vcf.gz; do
    
    SAMPLE_NAME=$(basename "${VCF}" .vcf.gz)

    OUTPUT_FILE="${OUTPUT_DIR}/${SAMPLE_NAME}_comparison.v4.2.first_pass"

    singularity exec docker://jmcdani20/hap.py:v0.3.12 \
        /opt/hap.py/bin/hap.py \
        -f "${BENCHMARK_BED}" \
        -r "${REFERENCE}" \
        -o "${OUTPUT_FILE}" \
        --engine="${ENGINE}" \
        ${PASS_ONLY} \
        -l "${REGION}" \
        HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz \
        "${VCF}"
done

The error:

INFO:    Using cached SIF image
[W] overlapping records at chr6:29747433 for sample 0
[W] Variants that overlap on the reference allele: 4
[I] Total VCF records:         4000097
[I] Non-reference VCF records: 4000097
[I] Total VCF records:         3956
[I] Non-reference VCF records: 3477
2025-03-04 17:57:41,658 WARNING  starting at chr1:151857523
2025-03-04 17:57:43,707 WARNING  No calls for location chr1:151857524-153780694 in query!
2025-03-04 17:57:43,707 WARNING  Creating template for vcfeval. You can speed this up by supplying a SDF template that corresponds to reference_for_assembly/hg38_MHC.fa

The variants inside this region exist, all the namings are correct. This works if I just pass chr1. But I cannot understand why it does not work on a specific region.

Thank you!!
Alisa

[alisamatisse]

strange, but the *first_pass.summary.csv is produced anyway