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?