Structural Variation Identification Using GRIDSS

[anitha-ravichandran]

Hello everyone,

I ran the GRIDSS tool for structural variation identification using the command: "$gridss" --jar "$gridss_jar" --reference "$Ref_dir" --output "$output_prefix".vcf.gz --threads 40 --blacklist "$blacklist" "$normal_file" "$tumor_file" on paired-end samples to detect somatic structural variants. However, the output VCF file contains only SVTYPE=BND, with no other SV types present. Does this indicate that all detected variants are breakends, with no other types of structural variants? Additionally, what further filtration and annotation steps should I take?