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This repository was archived by the owner on Apr 20, 2026. It is now read-only.
This repository was archived by the owner on Apr 20, 2026. It is now read-only.

Why ##reference=GRCh37/hg19 is added when working with GRCh38 #160

Description

@Manuel-DominguezCBG

Quick question

I am using this

apptainer exec --env PYTHON_EGG_CACHE=/mnt/scratch1/projects/Manuel_tmp/AI/10percent/Manuel_egg_cache \
    --bind /mnt:/mnt docker://pl92297/spliceai:2.0 spliceai \
    -I subset_10percent_sorted.vcf \
    -O subset_10percent_sorted_SpliceAI_3.vcf \
    -R ${bwarefgenomepath} \
    -A grch38

The version in that container is parser = argparse.ArgumentParser(description='Version: 1.3.1')

The container looks identical that your version 1.3.1.

The question that I have is why spliceai add this ##reference=GRCh37/hg19 when input VCF and the ${bwarefgenomepath} I used above are all GRCh38. I have checked with spliceAI lookup and the annotation is correct. Just wonder why this is added?

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