Advice needed in regards to the GRIDSS blacklist

[Teezi]

Hi,

I am new to use GRIDSS2 and want to check that I'm running the software correctly. From my understanding in relation to calling somatic structural variants following the QuickStart.md , gridss and gridss_somatic_filter will be used to call all SVs (raw outputs) and filter the raw outputs to just keep the somatic SVs, respectively.

In the 1st step (when using gridss), it's recommended that I use ENCFF356LFX.bed file for hg38 (UCSC chr notation) as the blacklist (exclude_list). Upon opening the hmf_dna_pipeline_resources.38_v5.34.tar.gz (which was downloaded from HMFTools-Resources in the Hartwig Medical Foundation's GCP bucket) I noticed another 2 blacklists: gridss_blacklist.38.bed.gz and sv_prep_blacklist.38.bed. Should I be using one of these lists instead of the ENCFF356LFX.bed and if so, which of the 2 files should I be using?

Many thanks in advance!!