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