The following files are included in the "hifisomatic_resources.tar.gz" resource bundle. ├── chr.bed├── GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta├── GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta.fai├── GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.dict├── human_GRCh38_no_alt_analysis_set.trf.bed├── refFlat.hg38.txt├── severus.jasmine.AN10.AC4.nosample.vcf.gz├── severus.jasmine.AN10.AC4.nosample.vcf.gz.tbi└── ensembl.GRCh38.101.reformatted.gff3.gz For the severus germline VCF, please cite the Human Pangenome Project paper: https://www.nature.com/articles/s41586-022-04601-8. Briefly, Severus 1.1 were used to generate a joint-call VCF from 159 control samples with the default parameters. The VCF was then merged with jasmine `--dup_to_ins` parameter. "human_GRCh38_no_alt_analysis_set.trf.bed" was downloaded from https://github.com/PacificBiosciences/pbsv/blob/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed. "GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta" was obtained from Wagner, J. et al. (Nat Biotechnol 2022). "chr.bed" is simply the start and end coord of each chromosome and was created manually using the genome size from the fasta index. "ensembl.GRCh38.101.reformatted.gff3.gz" is the Ensembl genes GFF file used by svpack to annotate gene and consequences of SVs. In addition, the repo contains two small demo dataset to test the workflow: "COLO829.30X.SV_region.bam" and "COLO829BL.30X.SV_region.bam" contains region in COLO829 cell lines that has 57 (out of 62) truth SV from Valle-Inclan et. al. 2022. "HCC1395.chr20.30X.bam" and "HCC1395BL.chr20.30X.bam" contains the chr20 region of HCC1395 cell lines.

v0.8: Switched from Sniffles to Severus for the control HPRC VCF. v0.6: Added ensembl gene GFF for svpack v0.4: Added ref fasta dict. v0.3: Fixed Sniffles background SV VCF.