Singularity, AnnotSV and HPO

Question

I am trying to use AnnotSV to annotate some Manta outputs in the following code with the HPO term changed:

Where:

• input_dir is the input directory
• singularity_container is the path to the AnnotSV singularity container

# Loop through the files in the input directory
for file in "$input_dir"/*.vcf; do
    # Get the base name of the file without extension
    filename=$(basename "$file" .vcf)

    # Create the output subdirectory within the input directory
    output_dir="$input_dir/AnnotSV_Batch_Run"
mkdir -p "$output_dir"

    # Set the output file path with "_AnnotSV" appended
    output_file="$output_dir/${filename}_AnnotSV_"

    # Run AnnotSV via Singularity with the base name as output prefix
    singularity exec "$singularity_container" AnnotSV -SVinputFile "$file" -genomeBuild GRCh38 --hpo "HP:0000001"  -outputFile "$output_file"
done

The HPO term I am using is in the jax.org site but when I run it - I get the most peculiar error option not known. but the HPO term is specified in the AnnotSV manual on page 49 (according to the number on the bottom). As for trying I tried with --HPOterm and hpoterm I tried with and without the : and with and without quotes as well. I am not sure what the issue is but I cannot seem to find the solution. Has anyone perchance used this software before with HPO terms as it seems not to be accepting the input I give it?

Answer 1

It seems that currently AnnotSV does not support HPO terms usage an Singularity.