#!/bin/bash -euo pipefail
# The Wave image (htslib_pysam_numpy_scipy) does not bundle scikit-learn,
# which VariantFilter needs to unpickle the RF model. Install it inline
# until the container is rebuilt with sklearn included.
python3 -m pip install --quiet --no-cache-dir scikit-learn joblib
nipt_score_vcf.py \
--vcf fetal_AF_40.vcf \
--bam fetal_AF_40.dedup.bam \
--ref Homo_sapiens_assembly38.fasta \
--rf-model model7_horizon_rf.pkl \
--output fetal_AF_40.snv.scored.vcf \
--sample-index 0 \
--rf-min-confidence 0.5 \
--model-version snv \
--fetal-fraction 0.4 \
--default-af 0.5 \
--gnomad gnomad_af.tsv.gz \