When I use smoove annotate, I just receive a MSHQ/SHQ of -1

[robertzeibich]

using smoove 0.2.7

GFF="Homo_sapiens.GRCh38.105.gff3.gz" # http://ftp.ensembl.org/pub/release-105/gff3/homo_sapiens/Homo_sapiens.GRCh38.105.gff3.gz

smoove annotate --gff ${GFF} ${outdir}/${SAMPLE}.vcf.gz | bgzip -c > ${outdir}/${SAMPLE}.annotated.vcf.gz"

Do you know why I just receive for MSHQ/SHQ -1? I am just using a single sample. Therefore, I asuume MSHQ and SHQ should be the same.

I will try the docker version next, but I am not sure if that will fix my issue.

Currently, I am using the RP+SR values in the VCF, but filtering on the calculated sum does not make sense.

My goal is to filter for high quality deletions.

Help is much appreciated.